Fmsarrpe (Sarrp Operator Manual)

SARRP
(Small Animal Radiation Research Platform)

Operator Manual
Language: English
About Xstrahl Xstrahl SARRP Operator Manual
About Us Gulmay Medical Inc. (an Xstrahl company) is a leading designer and
manufacturer of X-Ray research solutions used by life science
researchers and radiation physicists to further biological and cancer
research.
Xstrahl’s powerful and customizable SARRP (small animal radiation
research platform) is the most advanced, commercially available micro-
imaging X-Ray research system, while Xstrahl’s standalone X-Ray
Research Cabinets are often employed by research scientists to safely
irradiate both in vivo and in vitro biological samples.
Trademark Xstrahl® is a registered trademark of Xstrahl Limited.
Notice of Copyright SARRP Operator Manual ©2014 Gulmay Medical Inc (an Xstrahl
Company). All rights reserved.
Disclaimer Unless specifically agreed to in writing, Gulmay Medical Inc (an Xstrahl
company) assumes no liability for use of this document if unauthorized
changes to the content or format are made. Every care has been taken
to ensure the information in this document is accurate. However, Xstrahl
assumes no responsibility or liability for errors, inaccuracies or omissions
which may occur in this document.
To improve reliability, function or design, Xstrahl reserves the right to
change the product and/or this manual without notice.
Compliance The design of Xstrahl Systems is in compliance with internationally

recognized standards for safety.
File No., Issue, Date FMSARRPOM, Issue E©2014 Gulmay Medical Inc (an Xstrahl
Company). All rights reserved.
Contact Information
Web www.Xstrahl.com
Email support@Xstrahl.com
Phone +1 678-765-8970
Fax +1 678-765-8975
Technical Support
Email support@Xstrahl.com
Phone +1 678-765-8970
This document and all accompanying documents have all been drafted in
the English language.
Acknowledgments All manufacturer trade names and trademarks appearing in this

document are hereby acknowledged.
Referenced Documents Not all documents referred to in this document are part of the scope of
delivery for the equipment. Xstrahl reserves the right to determine the
documents delivered with the product.
FMSARRP Issue E©2014 Gulmay Medical Inc. (an Xstrahl Company) 8/9/14 i
All rights reserved.
Compatibility/
Contraindications SARRP Systems must be used only in combination with components
expressly recognized by Xstrahl as compatible with SARRP Systems. Before
using any equipment or component not supplied by Xstrahl Limited, consult
Xstrahl for advice on compatibility
The use of components other than those specified by Xstrahl may affect
electromagnetic compatibility (EMC) performance and result in increased
emissions or decreased immunity of the equipment.
Modification of
Equipment. Changes and/or additions to SARRP Systems must be performed only by
persons expressly authorized by Xstrahl. Such changes must comply with
best engineering practice and all applicable laws and regulations within the
jurisdiction.
Intended Audience The information contained in this manual is intended solely for the use of
trained and competent operators preferably trained by Xstrahl or an
authorized vendor. Training requirements vary by country. Users must
ensure that training is provided in accordance with all applicable local laws
and regulations.
Glossary This following glossary explains the acronyms, abbreviations and

special terms that could appear in this manual:
Glossary
A ampere (amp)
AC alternating current
AUX auxiliary
BB CT marker
BDM background debug mode
CB circuit breaker
CBCT cone beam CT
CE Conformité Européene
CCU central control unit
DC direct current
DMM digital multi-metre
EHT extra high tension
EMC electromagnetic compatibility
ESD electrostatic discharge
FS fuse
GUI graphic user interface
HT high tension
Hz Hertz
IEC International Electrotechnical
Commission
Kg kilogram
FMSARRP Issue E ©2014 Gulmay Medical Inc (an Xstrahl Company). 8/9/14 ii
Xstrahl SARRP Operator Manual About Xstrahl
Glossary
kV kilovolt
kW kilowatt
LCD liquid crystal display
mA milliampere (milli-amp)
mm millimetre
MU (radiation) monitor unit
mV millivolt
PC personal computer
PCB printed circuit board
PDF portable document file
PI plug
PPE personal protective equipment
PSU power supply unit
SK socket
sq square
SSD source-to-surface distance
SSR solid state relay
SW switch
TB terminal block
T/D time/dose
TFT thin film transistor
TP2 therapy panel 2
V volts
VA volts ampere
Vac volts A.C. (alternating current)
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl company).

iii 8/9/14 All rights reserved.
Warnings, Cautions and Notes
All potential hazards to the health of personnel and to the integrity of
Xstrahl’s equipment are presented as Warning and Caution notices.
All Warning and Caution notices in this manual will appear at the point of
application.
Sample Warning, Caution and Note:
WARNING: Warnings alert users to potential hazards to

personal health and safety. Each warning explains the
nature of the hazard, states the means by which the risk
can be avoided and explains the consequences of failing to
observe the warning.
CAUTION: Cautions alert users to the potential risk of

damage to the equipment or the environment, but not of
hazards to health and safety. Each caution explains the
nature of the hazard, the means by which the risk can be
avoided and explains the consequences of failing to
observe the caution.
Note: A note provides important information about the related content.
Specific Hazards SARRP Systems have system specific hazards that are a potential risk
to both personnel and equipment. All Specific Hazard notices in this
manual will appear at the point of application.
These specific hazard notices are:
RADIATION: Xstrahl X-Ray systems generate ionising

radiation which can cause death or injury if precautions are
not adhered to.
HIGH VOLTAGE: High voltages are present in all

Xstrahl X-Ray Systems when the system is connected to
the mains electrical supply. Exercise extreme caution and
isolate the mains electrical supply before attempting to
connect any cables or open any service or access doors on
equipment.
PROTECTIVE EARTH: Protective earth labels are

placed next to protective earth terminal studs. Ensure earth
terminals are connected to system earth at installation and
before operating the equipment. If any protective earth
point is disconnected, the equipment must not be used.
DANGER HIGH VOLTAGE; ISOLATE SUPPLY:

Before opening an access drawer, isolate the main supply.
High voltage components and wiring are present inside the
access drawer.
FMSARRP Issue E ©2014 Gulmay Medical Inc (an Xstrahl company). 8/9/14 iv
Xstrahl SARRP Operator Manual About Xstrahl
Safety All users/operators of this equipment must read, obey and understand all
safety warnings, cautions, notes and safety labels on equipment.
All users/operators must read and understand all information in this
document.
Intended Use (of equipment)

Xstrahl’s SARRP System is intended to be used in the delivery of
radiation to defined target volumes (biological research, cell samples or
aerospace research) while sparing surrounding normal tissue from excess
radiation
Intended Function
(of document). The intended function of this document is to assist the user in the safe and
correct operation, application and preventive maintenance of the
equipment. The user is the authority who has the control of the equipment
and the person(s) who operates and works on the equipment.
Xstrahl recommends this document be kept with the equipment at all

times.
Document
Amendment Table
Xstrahl, at their discretion, may update sections of this document after
first issue. Updated document amendments will be marked by an
identifying release date which can be found at the bottom of all document
pages (for example, 11/6/13).
It is the responsibility of the user to update the following Document
Amendment Table as new document amendments are
issued:
Document Amendment Table

No. Section Release Date Authorised By
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company). All rights 8/9/14 v
reserved.
—blank—
Xstrahl SARRP Operator Manual
Table of Contents
About Us .............................................................. (i)
Trademark ............................................................. (i) Intended Audience ............................................... (ii)
Notice of Copyright ............................................... (i) Glossary ............................................................... (ii)
Disclaimer ............................................................. (i) Warnings, Cautions and Notes ............................ (iv)
Compliance ........................................................... (i) Specific Hazards .................................................. (iv)
File No., Issue, Date ............................................. (i) Safety ................................................................... (v)
Acknowledgments ................................................. (i) Intended Use (of equipment) ............................... (v)
Referenced Documents ....................................... (i) Intended Function (of document) ......................... (v)
Compatibility/Contraindications ........................... (ii) Document Amendment Table .............................. (v)
Modification of Equipment ................................... (ii) Preface ................................................................ (xiii)
1 Precautionary Information ....................................................................... (1—1)

1.1 Ionising Radiation............................................................................................. (1—1)
1.2 Maintenance of Equipment............................................................................... (1—1)
2 SARRP Overview....................................................................................... (2—1)
2.1 SARRP Modules .............................................................................................. (2—2)
2.2 Safety System Interlocks.................................................................................. (2—3)
2.2.1 SARRP PC (Interface) and Supplementary Modules ............................ (2—3)
2.3 SARRP Training ............................................................................................... (2—4)
3 SARRP Control Interface Operator Manual ............................................ (3—1)
3.1 Robotic Specimen Stage Control ..................................................................... (3—2)
3.2 Homing the Stages ........................................................................................... (3—3)
3.2.1 Rotating the Entire Stage....................................................................... (3—4)
3.2.2 Starting the Homing Sequence .............................................................. (3—4)
3.3 Coordinate Systems ......................................................................................... (3—5)
3.4 Specimen Target Definition .............................................................................. (3—6)
3.4.1 Moving the Target .................................................................................. (3—6)
3.4.2 Robot Menu Options .............................................................................. (3—7)
3.5 X-Ray Control Software.................................................................................... (3—7)
3.6 Cone Beam CT (CBCT) Acquisition ................................................................. (3—8)
3.6.1 Calibration of the Flat Panel................................................................... (3—8)
3.7 Conducting a CBCT of a Specimen ................................................................. (3—9)
3.8 CBCT Reconstruction....................................................................................... (3—12)
3.9 View CBCT....................................................................................................... (3—13)
3.10 Locating the Target ........................................................................................ (3—14)
3.11 Cone Beam CT Menu..................................................................................... (3—15)
3.12 Imaging Panel Displays.................................................................................. (3—16)
3.12.1 ImageJ®............................................................................................... (3—17)
3.13 Irradiation Delivery ........................................................................................ (3—18)
3.13.1 To setup for Irradiation.......................................................................... (3—18)
3.13.2 To Irradiate following CBCT guidance with an Arc................................ (3—19)
3.13.3 To Irradiate following CBCT guidance with a Beam.............................. (3—20)
3.14 Troubleshooting.............................................................................................. (3—21)
3.14.1 Troubleshooting Error Table ................................................................ (3—21)
4 Examples of Irradiation Uses ................................................................... (4—1)
4.1 Example 1: Sequential Irradiation of Many Animals—Distal Femur ................. (4—2)
4.1.1 Method ................................................................................................... (4—2)
4.2 Example 2: Thorax Radiation Delivery ............................................................. (4—4)
4.2.1 Method ................................................................................................... (4—4)
4.3 Example 3: BB Quality Assurance.................................................................... (4—5)
4.3.1 Method ................................................................................................... (4—5)
Table of Contents Xstrahl SARRP Operator Manual
5 SARRP Quick Start Guide ........................................................................ (5—1)

5.1 Power On.......................................................................................................... (5—2)
5.2 Warm-up........................................................................................................... (5—2)
5.3 Starting SARRP................................................................................................ (5—3)
5.4 SARRP Control User Interface......................................................................... (5—4)
5.4.1 SARRP Robotic Specimen Stage .......................................................... (5—5)
5.4.2 SARRP X-ray Control Software . ............................................................ (5—5)
5.5 Cone Beam CT (CBCT) Acquisition ................................................................. (5—6)
5.5.1 Calibration of the Flat Panel................................................................... (5—6)
5.5.2 To Perform a CBCT ................................................................................ (5—7)
5.5.3 To Perform a FastScan .......................................................................... (5—10)
5.6 CBCT Reconstruction ....................................................................................... (5—10)
5.7 View CBCT ....................................................................................................... (5—11)
5.8 Locating the Target . ......................................................................................... (5—12)
5.8.1 To Locate a Target ……....................................................................... (5—13)
5.8.2 To Move to a Target Location ................................................................ (5—13)
5.9 Image Confirmation ......................................................................................... (5—14)
5.9.1 Simple Image Capture ........................................................................ (5—14)
5.9.2 Double Exposure Image Capture ........................................................ (5—15)
5.10 Irradiation Delivery …….................................................................................... (5—16)
5.10.1 To Setup for an Irradiation ………………........................................... (5—16)
5.10.2 To Irradiate Following CBCT Guidance with a Beam ........................ (5—17)
5.10.3 To Irradiate Following CBCT Guidance using an Arc ........................ (5—18)
5.11 BBQA Procedure ............................................................................................ (5—19)
5.12 Power Down SARRP..................................................................................... (5—20)
6 MuriSlice® Manual ................................................................................... (6—1)

6.1 MuriSlice Overview........................................................................................... (6—1)
6.1.1 Minimum Configuration Requirements ................................................... (6—2)
6.1.2 Installation .............................................................................................. (6—3)
6.1.3 Diagnostic Window................................................................................. (6—3)
6.2 Volume Visualisation: DigiOBS Module............................................................ (6—4)
6.2.1 Presentation of the Default GUI ............................................................. (6—4)
6.2.2 Management of Preferences.................................................................. (6—4)
6.2.2.1 Computation Tab ...................................................................... (6—5)
6.2.2.2 Interface Tab ............................................................................ (6—6)
6.2.2.3 Graphics Tab ............................................................................ (6—9)
6.2.2.4 DigiXST Tab ............................................................................. (6—10)
6.3 Operator Functions........................................................................................... (6—11)
6.3.1 Loading a Volume .................................................................................. (6—11)
6.3.2 Volume Visualisation.............................................................................. (6—12)
6.3.2.1 Multi-Display Visualisation........................................................ (6—12)
6.3.3 Managing a Volume ............................................................................... (6—13)
6.3.3.1 Display Management................................................................ (6—13)
6.3.3.2 Volume Alignment .................................................................... (6—15)
6.3.4 Data Management....................................................................... (6—16)
6.3.4.1 Saving and Exporting Volumes ................................................ (6—16)
6.3.4.2 Screen Dumps.......................................................................... (6—17)
6.4 Tomographic Reconstruction............................................................................. (6—19)
Table of Contents Xstrahl SARRP Operator Manual
6.4.1 Introduction ............................................................................................ (6—19)

6.4.2 Workflow Definition ................................................................................ (6—19)
6.4.3 Hardware Definition Toolbox.................................................................. (6—20)
6.4.3.1 Camera Definition Tab (Mandatory) ......................................... (6—20)
6.4.3.2 Geometry Calibration .......................................................................... (6—22)
6.4.4 Input ....................................................................................................... (6—26)
6.4.4.1 Input Definition (Mandatory) ..................................................... (6—26)
6.4.5 Output Definition (Mandatory) ................................................................ (6—28)
6.4.5.1 Volume Format and Name ....................................................... (6—28)
6.4.5.2 Volume Dimensions to be Reconstructed ................................ (6—28)
6.4.5.3 Region of Interest ..................................................................... (6—30)
6.4.5.4 Volume Resolution ................................................................... (6—30)
6.4.5.5 Cylindrical Reconstruction Constraint....................................... (6—31)
6.4.6 Reconstruction Grid Orientation............................................................. (6—32)
6.4.7 Reconstruction ...................................................................................... (6—32)
6.4.7.1 Filtered Back Projection............................................................ (6—32)
6.4.7.2 Post-Processing ....................................................................... (6—33)
6.4.8 Preview and Adjustment ........................................................................ (6—36)
6.4.8.1 Preview Settings....................................................................... (6—36)
6.4.8.2 Adjust ....................................................................................... (6—39)
6.5 Analysis of Cutting Planes: DigiCUT Plug-In.................................................... (6—41)
6.5.1 General Presentation of DigiCUT........................................................... (6—41)
6.5.2 DigiCUT Functionalities.......................................................................... (6—41)
6.5.2.1 Resolution ................................................................................ (6—41)
6.5.2.2 Contrast .................................................................................... (6—41)
6.5.2.3 Moving in the Image ................................................................. (6—41)
6.5.2.4 Other Features ......................................................................... (6—42)
6.5.3 Specific Slice Extraction Modules ........................................................... (6—48)
6.5.3.1 Cut Plane.................................................................................. (6—48)
6.6 Automation of Reconstruction Tasks: Batch Mode......................................... (6—49)
6.6.1 General Presentation ............................................................................. (6—49)
6.6.2 Batch Mode Functioning ........................................................................ (6—49)
7 Active DCAM Manual ............................................................................... (7—1)

7.1 Active DCAM Overview..................................................................................... (7—1)
7.2 Driver Setup …………………………................................................................ (7—2)
7.2.1 Installation ............................................................................................... (7—2)
7.3 1394b (FireWire 800) ....................................................................................... (7—6)
7.4 Registration....................................................................................................... (7—9)
7.5 User Interface................................................................................................... (7—10)
7.6 Properties Dialogue Box .................................................................................. (7—14)
7.6.1 Source ................................................................................................... (7—15)
7.6.2 Format .................................................................................................... (7—17)
7.6.3 Exposure ................................................................................................ (7—19)
7.6.4 Color ...................................................................................................... (7—21)
7.6.5 Advanced ............................................................................................... (7—23)
7.6.6 Display ................................................................................................... (7—25)
Appendix A: Notes ...................................................................................... (A—1)

Xstrahl SARRP Operator Manual Preface
Preface
This is the Xstrahl SARRP Operator Manual. This manual provides the information required to
operate a SARRP system.
Precautionary Information
1 This section provides precautionary safety information and warnings and must
be read and thoroughly understood prior to operating the SARRP system.
SARRP Overview
2 This section provides an overview of the SARRP system, including illustrations
of the SARRP modules, supplementary modules (PC and interface) and
descriptions of the safety system interlocks.
3 SARRP Control Interface Operator Manual

This section provides an overview of the SARRP interface, including
illustrations of interface screens.
Examples of Irradiation Uses

4 This section provides examples of irradiation uses. This includes
illustrations and potential methods of use.
SARRP Quick Start Guide
5 This section provides a quick overview of how to use the Xstrahl

SARRP. This includes how to power on, warm-up, run an exposure, calibrate
the system, irradiate a specimen (following CBCT guidance), image
confirmation, BBQA procedure.
MuriSlice®
6 This section demonstrates how to use the MuriSlice software. This includes
how to calibrate, reconstruct geometry configurations, visualise volumes and
meshes and manipulate 3D cutting planes.
Active DCAM
7 This section demonstrates how to use the Active DCAM software that works
with the Portal Camera. The user is able to adjust multiple camera parameters
in real time such as brightness, aim, shutter, camera, sharpness, view,
saturation and white balance.
xiv 8/9/14 FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).
Notes
A
About XSTRAHL
Refer to the About Xstrahl section at the front of this manual for general
information not covered in the manual sections.
Attachments
The following documents are included as a disc during the Initial Training Session:
• ImageJ User Guide

• AAPM Protocol for 40-300 kV X-Ray Beam Dosimetry in Radiotherapy and
Radiobiology (Journal Article)
• Cooling System Guide
• X-Ray Tube Guide
• MP1 Controller Guide
• PE Digital X-Ray Detector Guide
• GX Series (Generator) Technical Manual
• SARRP Technical Description
• SARRP Site Pre-Planning Guidelines
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company). 8/9/14
Section 1:
Precautionary Information
in this section
1.1 Ionising Radiation ...................................................................................... 1
1.2 Maintenance of Equipment ........................................................................ 1
1 Precautionary Information
RADIATION: X-Ray equipment emits ionizing radiation and is
dangerous to both operator and personnel. To avoid risk of injury, observe
all safety measures and ensure you are adequately trained prior to
operating this equipment.
The instructions in this manual should be thoroughly read and understood prior
to operating the SARRP system.
The SARRP system incorporates various safety features and components.

The operator should pay special attention to all safety warnings. Failure to
observe these instructions could result in serious injury to the operator and/or
public.
1.1 Ionising Radiation

Xstrahl’s X-Ray Systems produce ionizing radiation; therefore it is important to
protect the operator and the general public from exposure to unwanted and
excessive radiation during operation.
All operators must be fully acquainted with the relevant regulations and codes
of practice.
1.2 Maintenance of Equipment

As with all electro-mechanical equipment, various Xstrahl components
require periodic maintenance to ensure both operational safety and optimum
performance.
Failure to observe periodic maintenance can present a serious safety risk which
can result in serious injury to the operator and/or public.
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company). 8/9/14 1—1
Xstrahl SARRP Operator Manual Section 2: Precautionary Information
Section 2:
SARRP Overview
in this section
2.1 SARRP Modules ..................................................................................... 2
2.2 Safety System Interlocks ........................................................................ 3
2.3 SARRP Training...................................................................................... 4
2 SARRP Overview
RADIATION: X-Ray equipment emits ionizing radiation which
is dangerous to both operator and personnel in close proximity. To
avoid risk of injury, observe all safety measures and ensure you
are adequately trained power to operating this equipment.
The SARRP is a small animal irradiation platform used in radiobiology

science research for image-guided micro irradiation techniques (IGMI™).
It generates X-Rays up to 225 kV with a mA range of 0 to 30 mA and a
maximum power limit of 3 kW. The SARRP has a constant voltage 225 kV
X-Ray tube mounted on a motorized gantry.
Figure 2–1: SARRP Main Operating Area
2—2 8/9/14 FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).
Xstrahl SARRP Operator Manual Section 2: SARRP Overview
2.1 SARRP Modules

The SARRP is made up of the following modules:
SARRP System Modules
1 Emergency Stop Button 9 Specimen Stage
2 Start Button 10 Flat Panel Imager and Protection Shield
3 Stop Button 11 Portal Imager (not shown)
4 Cabinet Lights 12 Safety Interlock Circuit (not shown)
5 Lasers 13 SARRP PC (not shown)
6 Motors Bypass Off 14 MP1 Controller (figure 2-3)
7 X-Ray Tube 15 Warning Lamp Pillar (not shown)
8 Rotational Gantry
Figure 2–2: SARRP System
5
2
7 6
3
10
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).

8/9/14 2—3
Section 2: SARRP Overview Xstrahl SARRP Operator Manual
Figure 2–3: X-Ray Controller (MP1) Illustration
NOTE: The SARRP has an HT generator and cooling system. This is covered in more
detail in the SARRP Technical Manual provided with your equipment.
2.2 Safety System Interlocks

The Xstrahl SARRP has several built-in safety system interlocks:
SARRP Safety System Interlocks
Bunker Door Interlock The irradiation bunker door is also interlocked to the safety
circuit to prevent X-Rays from being initiated if the bunker door
opens.
X-Ray Controller (MP1) The X-Ray Controller (MP1) monitors the other hardware
aspects of the system and displays the associated error codes
on the screen. See the MP1 Controller Guide PDF included
with this manual for more information on the X-Ray Controller.
Warning Light The warning light is visible above a shielded unit or outside of
a bunker for an unshielded unit. This alerts the user that
X-Rays are on, or that the machine is ready for X-Rays to be
turned on.
2.2.1 SARRP PC (Interface) and Supplementary

Modules
The SARRP PC hosts the main interface used by the researcher, as
well as supplementary modules for other system components.
SARRP Supplementary Modules
Drivers Drivers for the EPID camera (point grey camera), webcam and
calibration camera.
GalilTools The DMC Smart Terminal runs the Galil stages. This software
is used for the initial setup of the unit and can be used for fault
finding purposes.
SARRP Control Interface Main user interface, including X-Ray control software.
ImageJ Software Used for image manipulation. Refer to the ImageJ User Guide
PDF included with this manual for more information.
MuriPlan Dose Planning System that allows for contouring, targeting,
DVH and viewing of the dose distribution..
MuriSlice User interface for capturing CBCT images, reconstructions and
creating Isocenters.
Xstrahl SARRP Operator Manual Section 2: SARRP Overview
2.3 SARRP Training

After the SARRP has been installed, an Application Specialist will perform both
operator and X-Ray safety training. This training will include the safety
information for the safety interlock system checks (to be performed periodically
by the user).
Radiation protection is recommended while using the SARRP (for example,
dosimetry badges).

8/9/14 2—5
Section 3:
SARRP Control Interface Operator Manual
in this section
3.1 Robotic Specimen Stage Control ............................................................ 2
3.2 Homing the Stages ................................................................................. 3
3.3 Coordinate Systems................................................................................ 5
3.4 Specimen Target Definition..................................................................... 6
3.5 X-ray Control Software……..................................................................... 7
3.6 Cone Beam CT (CBCT) Acquisition........................................................ 8
3.7 Conducting a CBCT of a Specimen ........................................................ 9
3.8 CBCT Reconstruction ........................................................................... 12
3.9 View CBCT ........................................................................................... 13
3.10 Locating the Target ............................................................................. 14
3.11 Cone Beam CT Menu ......................................................................... 15
3.12 Imaging Panel Displays ...................................................................... 16
3.13 Irradiation Delivery .............................................................................. 18
3.14 Troubleshooting .................................................................................. 21
3 SARRP Control Interface Operator Manual

WARNING: X-Ray equipment is dangerous to both the
operator and others working in proximity to the X-Ray system. To
avoid injury, observe all safety measures.
The SARRP Control Interface is a control software consisting of a main

graphical user interface control and several sub-interfaces for operating
different elements of the system.
The main interface (see Figure 3–1) performs the following

tasks:
• Controls the robotics stages (specimen stage)
• Acquires images for cone beam computed tomography (CBCT)
• Initiates CBCT reconstruction
• Locates the anatomical target
• Displays X-Ray images from flat panel and camera box
• Displays video images from the webcam
• Designates the target and delivers radiation and allows control of the
X-Ray delivery parameters
Xstrahl SARRP Operator Manual Section 3: SARRP Control Interface Operator Manual
Several other tasks are incorporated into the SARRP interface and will be
detailed further in this manual.
Figure 3–1: SARRP Control Interface Illustration
3.1 Robotic Specimen Stage Control
The SARRP provides 5º of freedom motion:
• 3 x translational stages for X, Y and Z motions of the animal specimen

• 1 x rotational stage for rotation of the animal and
• 1 x motor for rotation around the gantry axis
Before performing any motion, the SARRP must be able to communicate with
the robotic controller board. In the main SARRP control interface, there is a
check box labelled Connected (see Figure 3–2). If this check box is marked,
the SARRP control interface is able to communicate with the control board. If
the check box is unchecked, communication cannot be established and
troubleshooting is required.
Figure 3–2: User Interface
Section 3: SARRP Control Interface Operator Manual Xstrahl SARRP Operator Manual
3.2 Homing the Stages
CAUTION: The robotic stage must be in the Origin position before

homing the stages.
Homing is the procedure which initializes the absolute position of each stage
and motor. This procedure is required every time the system is powered on or
the control board is reset.
The software is capable of distinguishing whether homing is required or not. If

robot homing is required, the motors will not enable and this is further
indicated by the Motors Enabled check box in the main interface (see Figure 3–
2). If the robot is not homed, checking this box will cause a pop-up window to
be displayed showing the proper arrangement of the rotational stage (cable
carriers) prior to beginning the homing procedure (see Figure 3–4).
Figure 3–3: Homing: Rotational Stage Arrangement
Figure 3–4: Circular Gear Arrangement
The operator must manually position the rotational stage (see Figure 3–4) prior
to homing the robot. If the position of an axis needs adjusting, the black circular
gears at the end of each stage can be rotated to move the required axis.
3.2.1 Rotating the Entire Stage

The theta gear is located to the left of the vertical column. Rotate the entire
stage ± 180º. In most cases, the user can rotate the stage by hand manually.
3.2.2 Starting the Homing Sequence

Once the stage positions have been checked, selecting OK will start the
homing sequence. Each stage axis (including the gantry) will now move or
rotate.
Once the homing sequence is completed, the Motors Enabled Check Box will
be checked and the robot stages can be programmed. This box can also be
used to enable/disable the motors.
3.3 Coordinate Systems
The SARRP system has two coordinate systems:

• The SARRP CT coordinate system and
• a robot coordinate system.
Figure 3–5: SARRRP CT Coordinate System
Figure 3–6: Robot Coordinate System
The previous diagrams illustrate the direction of the robotic specimen stage
about the isocenter with the relevant ± value entered into the axis boxes.
The user interface is designed to work primarily with the SARRP CT

coordinate system. All positions displayed or accepted by the main interface
are in this coordinate system.
Figure 3–7: User Interface with ISO and Gantry Selection
It is also possible to specify/display the position in the robot coordinate system

by using the Move Joints option in the Robot sub-menu of the main toolbar (see
Figure3–8). This action is not recommended unless it is necessary to move
robot motorsindependent of the image guidance system.
Note The robot coordinate system is defined based on the readings of the robot
motor encoders; its origin is based on the home position of the robot.
Robot Joints is used in the initial configuration of the unit and calibration
procedures.
Figure 3–8: Moving Robot Stages and Motors in Coordinate System1
3.4 Specimen Target Definition
Positioning of targets is performed through the main panel. A target is defined as

the specific joint that is moved to the beam isocenter (and is then irradiated).
Figure 3–9: CBCT Coordinates
This point is defined in the CT coordinate system and is moved to the beam
isocenter by moving the robotic stage. The current position of the target is
demonstrated in five display boxes to the right of the ISO CT label.
3.4.1 Moving the Target

There are four entry fields labelled ISO Goal where the target goal position can
be entered in millimeters and degrees. When using MuriSlice, the required
values are populated by the software and do not need to be manually entered.
The drop-down menu also includes a text box to define the gantry angle in
degrees. Selecting the Move button moves the target to the isocenter, and the
numbers in ISO CT and ISO Goal will be equal.
Note Pressing the STOP button at any time prevents further motion of the robot.
1. Independent of CT guidance.
3.4.2 Robot Menu Options

The Robot menu in the main interface toolbar provides two more options:
Robot Menu Options

Change Speed/Accel The Change Speed/Accel menu option changes the speed
Option and acceleration of the robot
The Unhome Robot menu option rehomes the robot (if not
Unhome Robot Option
already properly homed).
Figure 3–10: Robot Speed and Accel/Decel Settings
3.5 X-Ray Control Software
The X-Ray Control Software allows the computer to talk to the MP1. It offers quick setup
for CBCT and irradiation of the specimen. All safety conditions must be met before X-
Rays are turned on. Any interruption of the safety circuit will disable X-Rays. The X-
Ray control software has a menu for Technique Presets which enables a user to define
a kV and mA setting for each condition used.
To define the presets, go to C:/SARRP_Data/PresetData.txt. The name, kV, mA, focus

and time can be defined in this menu.
Figure 3–11: Technique Presets
3.6 Cone Beam CT (CBCT) Acquisition
On-board CBCT imaging is achieved by a 360º rotation of the horizontal animal between
the stationary X-Ray source and the 20 x 20 cm flat panel detector.
CBCT is conducted without the collimator fitted and with the 1 mm of aluminum filter
fitted.
3.6.1 Calibration of the Flat Panel

Before the first CBCT acquisition, it is necessary to calibrate the flood field and dark field
gains of the flat panel detector. This is completed each time a new imaging kV and mA
setting is desired.
To calibrate the flat panel:
1. Rotate the gantry to 90 degrees. Select the Imaging Parameters (aluminum filter,
Fine Focus, desired kV and mA). Pull up the Detector Shield. Ensure nothing is in
the path from the tube to the detector.
2. Select Detector Calibration from the Detector sub-menu in the main toolbar.
3. A prompt will appear stating the X-Rays must be off for the beginning of the process
(Figure 3-12). This will acquire a dark field image.
4. Then SARRP will alert the operator that the X-Rays will be turned on. Select OK (at
the prompt) to turn X-Rays on for capturing a flood field image.
5. After completing the calibration process, the interface will display a prompt advising
X-Rays will be turned off (Figure 3-13).
Figure 3–12: Detector Calibration Process
Figure 3–13: Detector Calibration Completed
8/9/14 FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).
3—8
3.7 Conducting a CBCT of a Specimen
A CBCT can be conducted for a new series or scans added to an existing study.
To perform a CBCT:
Note: Always begin a CBCT with X, Y, and Z at 0 degrees. Using the SARRP
software, Experiment and Scan names must contain NO SPACES.
1. Place the specimen on the robotic stage.
2. If necessary, adjust the position of the specimen to bring the desired target into the
field of view. The lasers on the SARRP system can be used for visual confirmation of
the center of the field of view
3. Select the Imaging Parameters (aluminum filter, Fine Focus, desired kV and mA). Pull
up the Detector Shield. Move Gantry to 90 degrees.
4. Either choose a defined Experiment in the drop down menu or select New Experiment
from the main interface (Figure 3-14). If a New Experiment is chosen, define the
name in the popup menu (Figure 3 –14) and click OK.
Figure 3–14: Creating a New Experiment for Performing New CBCT Scans.
5. Click CBCT Acquisition on the main interface. If the gantry is not at 90º, a prompt will
alert the user that the gantry is moving to 90º.
6. A pop-up window will prompt for a name for the new scan. The operator can choose
the default name or type the desired name. Click OK to accept.
FMSARRP Issue E ©2014 Gulmay Medical Inc (an Xstrahl Company). 8/9/14 3—9
7. A prompt will ask the user if the robotic stage is free to move. This ensures any
cabling is accounted for. Also this will verify that the controller is in X-ray control
mode (802) and the key is in High Tension.
Figure 3–15: CBCT Ready
WARNING: X-Ray equipment emits ionising radiation which is

dangerous to both operator and personnel in close proximity. To avoid
risk of injury, observe all safety measures and ensure you are
adequately trained prior to operating equipment.
8. In the CBCT window, the interface will prompt for the number of 2D projections
(default is 360º; one projection at each degree of rotation), Figure 3–16. The default
couch speed default is 6º per second for a 360 projection scan. The speed can be
slowed down, but it is not recommended to go any higher. Select the reconstruction
protocol from the drop-down menu list (Figure 3–16). Click OK to start the acquisition
Imaging Protocols
Level of Resolution Number of 2D Projections Approximate Dose
Low 360 1.2cGy
Medium 720 2.4cGy
High 1440 4.8cGy
Figure 3–16: CBCT Setup Parameters
3—10
9. The interface will display a progress bar displaying the image acquisition process
and a completion message at the end of the acquisition (Figure 3–17).
Figure 3–17: Completing CBCT
To perform a FastScan CBCT:
A FastScan allows the user to grab projections in 180 degrees plus the fan angle to
reduce the imaging dose by 45% compared to a 360 degree projection. This is useful for
researchers concerned about imaging dose or creating fractionated treatments.
1. First select the desired Experiment in the drop down menu or choose a New
Experiment. Then select the Cone Beam CT Menu and choose the FastScan
option.
Figure 3–18: Select FastScan
2. The CBCT parameters will look the same, but the number of projections will be set to
199. Be sure to choose the FastScan Reconstruction protocol.
Figure 3–19: FastScan Parameters
3.8 CBCT Reconstruction
CBCT reconstruction is performed in parallel with CBCT acquisition. While the progress
bar (see Figure 3–17) displays the image acquisition, the MuriSlice is launched and
performs reconstruction. It uses a FDK algorithm on a Tesla GPU. Many reconstruction
protocols can be made with the different filters and voxel sizes offered.
The MuriSlice Manual (Section 6) presents the steps required to perform CBCT
manipulation.
3—12
3.9 View CBCT
If the CBCT MuriSlice window does not launch automatically, View CBCT can be used to
view a CBCT scan in the MuriSlice software.
To view a CBCT scan:
1. Select the experiment via the drop-down menu (see Figure 3–20) in the main
interface panel.
2. Click the View CBCT button (see Figure 3–20) located in the CBCT acquisition
area. If there is more than one CBCT scan for the current experiment, the software
will prompt to choose the CBCT scan from a drop-down menu (see Figure 3–20). It
will then ask which reconstruction protocol is desired for the specific scan chosen.
Figure 3–20: Steps to View an Available CBCT Volume
3.10 Locating the Target
When the CBCT reconstruction is complete, the target can be located in the MuriSlice
window (see Figure 3–21).
Figure 3–21: Locating the Target in the MuriSlice Window
Note For a more complete list of MuriSlice functions, consult the About tab, Getting
Started section.
The coordinates of the target are displayed in the pixel value window.
To locate a target:
1. Select Auto in the scan window (right menu) to automatically change the
contrast. Contrast can also be manually changed using the sliding bars for white
and black.
2. Select an isocenter by left clicking in a planar window at the desired target location. Verify
in all 3 planar windows that the target is properly placed. Then select Create from the List of
Reference Points (right menu) to create the Isocenter. Choose a name and click OK.
3. You will need to know which angle you want to irradiate. Measure the distance
from the surface of the specimen along the point of Radiation Entry of the target
by selecting a new target at the surface of the specimen. This can be called “Skin to
Isocenter at Gantry x”. Then select the isocenter and the newly created point at the
surface of the skin by holding down ctrl and left click both names. The distance
between the two will be just above the create button.
3—14
To move to a target location:
1. Select Accept Coordinates in the MuriSlice window (Figure 3–21) to pass on these
coordinates to the SARRP interface (Figure 3–22).
2. Click OK in the main interface (Figure 3–22) to accept coordinates as the new
isocenter goal.
3. Select Move to relocate the target to the beam isocenter (for example, ISO CT will be
equal to ISO goal).
Figure 3–22: Coordinates of the Target Received from MuriSlice
3.11 Cone Beam CT Menu
There is a CBCT sub-menu in the main menu bar, which is designed to provide access
to additional CBCT functionality (see Figure 3–23).
Figure 3–23: Cone Beam CT Sub-Menu
The first option in the list is FastScan. This offers a scan using 199 degrees while still
giving a great resolution scan. It decreases the scan dose by 45%.
The second item in the CBCT sub-menu is Re-Reconstruct. This initiates the CBCT
reconstruction procedure and provides the option of performing reconstruction with
different protocols.
The third CBCT menu item is CBCT Calibration. This is where a technician calibrates
the panel to ensure the CBCT space is aligned with the mechanical space.
3.12 Imaging Panel Displays
The main interface has two imaging panels:
Imaging Panels
Bottom Left Image The first image panel is located at the bottom left of the main interface
Panel and displays the SARRP workspace. This panel is directly connected
to the optional camera mounted on the passive arm. By relocating the
passive arm, the field of view of this camera can be adjusted to different
working areas of the SARRP (see Figure 3–24)
Bottom Right The second imaging panel is located at the bottom right of the main
Image Panel interface. This panel is a notebook with four tabs; Flat Panel, Portal
Image, Calibration and CT Viewer (see Figure 3–24). Each tab is
associated with corresponding hardware.
Flat Panel captures an image from the X-Ray flat panel detector and CT
Viewer (for example, the one used for CBCT imaging). This tab has a
check box for displaying the beam centre; the Portal Image tab displays
the image captured by the X-Ray camera box located beneath the
subject.
This camera is oriented orthogonal to the flat panel and is used for
anterior-posterior imaging of the subject. Both tabs have a Capture
Image button for capturing the image and a Save Image button for
saving the image to a file. The third tab, Calibration, is used for
displaying the image from a calibration camera and is not used for
normal operation of the SARRP.
The fourth tab is CT Viewer. This enables the user to view an already
created CBCT only if the dose has been computed and it has been
loaded into Slicer. This is verification for CBCT.
Figure 3–24: Image Panel Tabs
3—16
The Detector Option on the main interface toolbar has three image
related sub-menus:
• The first detector menu item is Detector Calibrate, which enables the user to
calibrate the flat panel for each kV and mA used.
• Shut Down the Detector enables the user to stop operation of the Detector panel,
which causes the SARRP interface to release the detector so it can be used by an
external software.
One software is provided by the panel manufacturer and may be used for
capturing images without using the SARRP software. If the detector is released by
the SARRP software (for example, by clicking Shut Down the Detector), it should
be reattached through the Initialize the Detector option in the Detector sub-menu
before attempting to capture images from the flat panel.
Figure 3–25: Detector Sub-Menu
3.12.1 ImageJ®
ImageJ is a free software package used for image processing. The SARRP software
provides a link to this external software, which is used to open images captured by either
the flat panel or X-Ray box camera.
The main toolbar has an ImageJ sub-menu, which includes options to start the
ImageJ software.
3.13 Irradiation Delivery
SARRP has multiple methods of delivery:
Methods of Irradiation Delivery
Conformal Arc Conformal arc therapy is possible with SARRP. The X and Y
Therapy (Conventional coordinates of the robot are continuously adjusted to keep the
and Conical) target at the isocenter. Radiation from either the Theta or Gantry
angles can be performed by use of the Continuous Arc Motion
menu.
Direct Radiation Using Beams, the coordinates of the target are read by the software
(Beams) from the selection using the CBCT image. After selecting the Theta
and Gantry angles for the beam, the user selects Move in the
SARRP Software to setup for an irradiation.
The Delivery sub-menu has a Dose Calculator designed to calculate the exposure time
based on the radiation parameters specified by the user.
These parameters include collimator size, source-to-surface distance (SSD), dose depth
and desired dose (Figure 3–18). After a calculation is complete, Apply Setting enables the
user to send the kV, mA and exposure time to the X-Ray control software.
Figure 3–26: SARRP Dose Calculator
3.13.1 To Setup for an Irradiation

1. Change the filter to the copper filter and put the Detector Shield in place.
2. Select a preset or set the parameters on the controller (MP1). Check broad focus,
220 kV, 13.0 mA and enter the exposure time.
3—18 8/9/14 FMSARRP Issue E ©2014 Gulmay Medical Inc (an Xstrahl Company).
3.13.2 To Irradiate following CBCT guidance using an Arc:
1. Ensure the subject has been moved to the chosen Isocenter.
2. Place the Collimator with the selected Nozzle size.
3. Select Continuous Arc Motion from the Delivery sub menu (the main interface
toolbar).
4. Enter the Gantry Start and Stop angles for a Conventional Arc Treatment. For a
Conical Arc treatment, verify the Gantry is not at 0 degrees and both Start and Stop
are the same. Change the Couch Start and Stop angles. Choose to either enter the
time or the speed and the other will automatically fill in.
Figure 3–27: Continuous Arc Motion
5. When you choose Perform Arc Motion, the Gantry or Couch will automatically move
to the Start Location. If the motors are stopped by the user during setup, then the
Arc Motion needs to be exited and started over.
6. When the SARRP software alerts of X-Rays imminent, press OK when ready.
Figure 3–28: ARC X-Ray On
3.13.3 To Irradiate following CBCT guidance with a Beam
1. Select Dose Calculator from the Delivery sub-menu (the main interface toolbar)
(Figure 3–26).
2. Enter the Collimator, SSD (Source to Skin Distance), Depth (in tissue) and Dose.
3. Choose Calculate.
4. When Apply Setting is chosen, the kV, mA, Broad Focus and Exposure Time are
automatically sent to the X-ray control Software.
5. Ensure the subject has been moved to the chosen Isocenter. Move the Gantry to
the chosen Treatment Direction.
7. Press X-rays on to complete the treatment.
Figure 3–29: Irradiation with Dose Calculator Setup
3.14 Troubleshooting
The most common error message is demonstrated in Figure 3–30. This error occurs when
the software cannot send the command to the control board.
Figure 3–30: Robot Error
Troubleshooting the Robot error:
1. Does the software still communicate with the control board? Is Connected marked
in the check box (see Figure 3–2)?
2. Is the Robot obstructed by an object and can it move freely?
3. Are any of the joints at the travel limit? If so, manually move the joint away from the
limit.
4. Exit the SARRP software and restart.
5. Exit the SARRP software and reset the control board by cycling power to the SARRP
and restarting.
3.14.1 Troubleshooting Error Table

SARRP error table with corresponding action response:
Troubleshooting Error Table
System Error Action Required

Motor power is off Release stop button and re-enable motor power
Amplifier error Restart system; if the problem persists, contact Xstrahl.
Motor is enabled Enable motor power; if not successful, restart system
Robot is not homed Restart SARRP software
Out of limits Manually move joint within limits
System error If error persists, contact field service
Motion, parameter (speed, Change parameter to valid value

accel or decel) out of range
3. Error indicates commands cannot be sent to the control board.
Section 4:
Examples of Irradiation Uses
in this section
4.1 Example 1: Sequential Irradiation of Many Animals—Distal Femur ............ 1
4.2 Example 2: Thorax Radiation Delivery......................................................... 4
4.3 Example 3: BB Quality Assurance ............................................................... 5
4 Examples of Irradiation Uses

The SARRP offers the most sophisticated treatment options available for small
animal irradiation research.
When reviewing the methods in this section, it is important to understand that the
procedures outlined here are specific examples of SARRP applications that have
helped researchers accomplish specific research objectives.
Because the SARRP offers varied equipment and capabilities, many different
applications can be tailored from these examples using similar procedures, but with
small adjustments, for example, the double exposure method outlined in Example 1
(section 4.1) is used heavily in many applications which do not require the accuracy
and precision of CBCT-guided irradiation.
Xstrahl SARRP Operator Manual Section 4: Examples of Irradiation Uses
4.1 Example 1: Sequential Irradiation of Many Animals: Distal Femur
The strength of the SARRP system lies in its ability to precisely irradiate several
animals in a short amount of time.
4.1.1 Method
SARRP: high dose output and speedy imaging
Our group targeted 4 Gy fractions of radiation to only the distal portion of the femurs of
27 mice in under 2.5 hours. SARRP takes advantage of its high dose output, as well
as speedy imaging process to accomplish this task.
The adult mouse femur is roughly 1.3—1.5 cm in length. Mice were set up prone on a
styrofoam platform, with the limbs extended and fastened to the surface using surgical
tape. Anaesthesia was continuously administered through tubing into a makeshift
hood composed of tape surrounding the mouse’s head.
In order to target the region distal to the femur (see Figure 4–1), we employed the
X-Ray camera and ImageJ image processing software.
Firstly, an open field image was acquired; the two images were overlain to obtain a
double exposure displaying clearly, the positioning of the beam with respect to the
anatomy of the mouse. Minor adjustments were made by translating/rotating the
stage to properly situate the target region of the femur into the radiation field.
At this point, the energy settings of the beam were adjusted to treatment energy
(225 kVp and 13.0 mA) and radiation delivered. In order to reduce the setup time and
uncertainty, the styrofoam stage was marked where the irradiated leg was positioned so
that the next mouse could be taped down roughly where the previous mouse was, thus
cutting down on the distance the stage needed to be moved to align the beam.
Figure 4–1: Setup Confirmed by X-Ray Camera
Section 4: Examples of Irradiation Uses Xstrahl SARRP Operator Manual
Figure 4–2: User Interface (Femur)
The user interface allows the user to change the isocenter and gantry angles.
Xstrahl SARRP Operator Manual Section 4: Examples of Irradiation Uses
4.2 Example 2: Thorax Radiation Delivery
Lung radiation (either unilateral or bilateral) can be delivered in a high-throughput

manner.
4.2.1 Method
We used a large collimator (see Figure 4–3) with an aperture of 1.4 cm x 2.5 cm, and to
visualize the lungs, we used the X-Ray Box camera (SARRP interface) with beam
settings of 100 kVp and 5.0 mA without copper filtration.
Once the mouse was placed in the proper position (lungs fully covered), we delivered the
therapy beam (220 kVp, 13.00 mA, 0.15 Cu). Alternatively, the beam coverage can be
shifted by moving the stage through the SARRP Control Interface menu (see Figure 4–4)
to cover only half of the thoracic region.
It may help the user to image the whole thorax first to visualize the mid-line, then to shift
so that the edge of the beam coincides with the mid-line.
Figure 4–3: Beam Position Superimposed (Midsection)
Figure 4–4: User Interface (Thorax)
The user interface enables the user to change the isocenter and gantry angles.
4—4 FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).
8/9/14
Section 4: Examples of Irradiation Uses Xstrahl SARRP Operator Manual
4.3 Example 3: BB Quality Assurance
To assure the accuracy of the CT-Beam calibration, we ran a daily quality assurance
routine which took approximately 15 minutes (and should be accomplished before
delivery of CBCT guided radiation).
4.3.1 Method
We used a semi-rigid mouse holder to which we affixed a piece of styrofoam, embedded
a BB and placed on the SARRP stage (see Figure 4–5). We then acquired a CBCT of this
setup. Using the MuriSlice software, we navigated through the reconstructed volume and
locate and target the BB. We then attached a 5 x 5 collimator through which we see a
beam’s eye view.
In order to acquire a measure of accuracy, the BB was aligned for and imaged in two
gantry positions: 90º and 0º. Flat field images were taken using the flat panel image and
the portal view tabs in the SARRP interface.
To properly evaluate these images, they should be saved in a directory and opened
using the java-based freeware, ImageJ. ImageJ makes it possible to set a scale using the
measure bar (see Figure 4–6). Because we know the width of our collimated beam is 5
mm, we used this as a reference for a measure bar.
Using both images (90º and 0º) we obtained offsets in X, Y and Z, and recorded these
measurements.
Figure 4–5: Quality Assurance Setup: CT Beam Calibration
Figure 4–6: Quality Assurance: Measuring BB Offsets from

Centre
Section 5:
SARRP Quick Start Guide
in this section
5.1 Power On ................................................................................................. 2
5.2 Warm-up .................................................................................................. 2
5.3 Starting SARRP ....................................................................................... 3
5.4 SARRP Control User Interface ................................................................. 4
5.5 Cone Beam CT Acquisition ...................................................................... 6
5.6 CBCT Reconstruction............................................................................... 10
5.7 View CBCT …………………..................................................................... 11
5.8 Locating the Target .................................................................................. 12
5.9 Image Confirmation................................................................................... 14
5.10 Irradiation Delivery..................................................................................... 16
5.11 BBQA Procedure ....................................................................................... 19
5.12 Power Down SARRP.................................................................................. 20
5 SARRP Quick Start Guide
RADIATION: A SARRP system generates ionizing radiation which can

cause death or injury if precautions are not adhered to.
HIGH VOLTAGE: High voltages are present in all SARRP systems

when connected to the mains electrical supply. Exercise extreme
caution and isolate the mains electrical supply before attempting to
connect any cables or open any service or access doors on the
equipment.
This quick start guide enables the operator to understand the basic steps involved in
using the SARRP. The guide will focus on powering up, warming up, calibration of
the flat panel, imaging a subject, setup for irradiation, image verification, completing
irradiation, performing a BBQA test and powering down the SARRP.
5.1 Power On
To power on the SARRP:
1. Turn on the mains isolator, if present.
2. Insert the key into the X-Ray controller—turn the key to the Standby
(Position 2) location.
3. Turn SARRP on by pressing the on switch located on the SARRP frame. This will
power the system electronics and cooling system. The mains light (on the MP1) will
be illuminated.
4. Turn the key on the X-ray controller to High Tension (Position 3).
Note Ensure the cooling system is also Powered On.
5.2 Warm-up
Once the SARRP is powered on, a warm-up must be completed.
CAUTION: Ensure the PE X-Ray Protector panel is in place prior to

commencing the system warm-up. If X-Rays On is pressed without the
panel in place, error code 16 will be displayed on the controller.
Note Ensure the X-Ray bunker door is closed and the safety interlocks enabled.
The X-Ray controller (MP1) will display program 810 or 811 when powered on at the
start of the day. Program 810 is a short run on the MP1. This is used for daily warm-ups
and takes approximately 17.5 minutes. If the MP1 has not been used for a while, then a
811 program is required. The long warm-up takes 72 minutes to complete.
To conduct a warm-up of the X-Ray tube:
The MP1 will display program 810 when powered on at the start of the day.
If the MP1 does not automatically start with program 810:

Press the SET button on the MP1 and type 810 then ENTER. The program selected
and will display the kV, mA and time required for the warm-up sequence. This is
approximately 17.5 minutes for a daily warm-up.
 Turn the key (MP1) to HT (position 3) and press X-Ray On on the X-Ray control
area of the SARRP control interface. The controlled area light will illuminate and
the X-Ray On light will flash during the exposure. The X-Ray light will illuminate on
the front panel of the MP1.
8/9/14
5.3 Starting SARRP
Once a warm-up has been run, the SARRP is ready to operate for Imaging and
Irradiation.
To start the SARRP:
1. At the end of the warm-up, the MP1 will default to program 802. If it does not
default to program 802, type Set 802 and Enter.
2. Open the SARRP user interface (desktop shortcut) on the PC. SARRP will now
conduct its homing sequence—ensure the stage’s position mirrors the image on the
screen.
Note SARRP must complete a homing sequence before the user can conduct any
imaging or irradiation protocols.
Figure 5–1: Homing Image
3. At the end of homing, all coordinates of the platform will automatically move to its
origin location.
5.4 SARRP Control User Interface
The main interface (see Figure 5–2) performs the following tasks:
• Controls the robotics stages (specimen stage)
• Acquires images for cone beam computed tomography (CBCT)
• Initiates CBCT reconstruction
• Accepts coordinates from a SARRP CBCT
• Displays X-Ray images from flat panel and camera box
• Displays video images from the webcam
• Designates the target and delivers radiation and allows control of the X-Ray
delivery parameters
Figure 5–2: SARRP Control Interface Illustration
8/9/14
5.4.1 SARRP Robotic Specimen Stage
The SARRP provides 5º of freedom motion:
• 3 x translational stages for X, Y and Z motions of the animal specimen

• 1 x rotational stage for rotation of the animal and
• 1 x motor for rotation around the gantry axis
Before performing any motion, the SARRP must be able to communicate with the
robotic controller board. In the main SARRP control interface, there is a check box
labelled Connected (Figure 5–3). If this check box is marked, the SARRP control
interface is able to communicate with the control board. If the check box is unchecked,
communication cannot be established and troubleshooting is required.
Figure 5–3: User Interface
5.4.2 SARRP X-ray Control Software

The X-Ray Control Software allows the computer to talk to the MP1. It offers quick setup
for CBCT and irradiation of the specimen. All safety conditions must be met before X-
Rays are turned on. Any interruption of the safety circuit will disable X-Rays. The X-
Ray control software has a menu for Technique Presets which enables a user to define
a kV and mA setting for each condition used.
To define the presets, go to C:/SARRP_Data/PresetData.txt. The name, kV, mA,

focus and time can be defined in this menu.
Figure 5–4: Technique Presets
5.5 Cone Beam CT (CBCT) Acquisition
On-board CBCT imaging is achieved by a 360º rotation of the horizontal animal between
the stationary X-Ray source and the 20 x 20 cm flat panel detector.
CBCT is conducted without the collimator fitted and with the 1 mm of aluminum filter
fitted.
Note The best imaging values are between 50 to 75 kV and below 1.0 mA.
5.5.1 Calibration of the Flat Panel

Before the first CBCT acquisition, it is necessary to calibrate the flood field and dark field
gains of the flat panel detector. This is completed each time a new imaging kv and mA
setting is desired.
1. Select the Imaging Technique Preset on the X-ray Control Software. Place the
Aluminum filter on the tube head. Pull up the Detector Shield. Rotate the gantry
to 90 degrees. Ensure nothing is in the path from the tube to the detector.
2. Select Detector Calibration from the Detector sub-menu in the main toolbar.
3. A prompt will appear stating the X-Rays must be off for the beginning of the process
(Figure 5-5). This will acquire a dark field image.
4. Then SARRP will alert the operator that the X-Rays will be turned on. Select OK (at
the prompt) to turn X-Rays on for capturing a flood field image.
5. After completing the calibration process, the interface will display a prompt advising
X-Rays will be turned off (Figure 5-6).
Figure 5–5: Detector Calibration Process
Figure 5–6: Detector Calibration Completed

5—6 8/9/14 All rights reserved.
5.5.2 To Perform a CBCT
Note: Always begin a CBCT with X, Y, and Z at 0 degrees. Using the SARRP
Control Interface Software, the Experiment and Scan names must contain
NO SPACES.
1. Place the specimen on the robotic stage. Ensure the nose of the subject is facing
the operator.
2. If necessary, adjust the position of the specimen to bring the desired target into the
field of view. The lasers on the SARRP system can be used for visual confirmation of
the center of the field of view.
3. Select the Imaging Technique Preset on the X-ray Control Software. Place the
Aluminum filter on the tube head. Pull up the Detector Shield and pull the Panel
housing forward to the hard stop. Rotate the gantry to 90 degrees.
4. Either choose a defined Experiment in the drop down menu or select New Experiment
from the main interface ( Figure 5-7). If a New Experiment is chosen, define the name
in the popup menu (Figure 5–7) and click OK.
Figure 5–7: Creating a New Experiment for Performing New CBCT Scans.
5. Click CBCT Acquisition on the main interface. If the gantry is not at 90º, a prompt will
alert the user that the gantry is moving to 90º.
6. A pop-up window will prompt for a name for the new scan. Click OK to accept the
default name or type the desired name.
7. A prompt will ask the user if the robotic stage is free to move. This ensures any
cabling is accounted for. Also verifies that the controller is in X-ray control mode (802)
and the key is in High Tension.
Figure 5–8: CBCT Ready
WARNING: X-Ray equipment emits ionizing radiation which is

dangerous to both operator and personnel in close proximity. To avoid
risk of injury, observe all safety measures and ensure you are
adequately trained prior to operating equipment.
8. In the CBCT window, the interface will prompt for the number of 2D projections
(default is 360º; one projection at each degree of rotation), Figure 5–9. The default
couch speed default is 6º per second for a 360 projection scan. The speed can be
slowed down, but it is not recommended to go any higher. Select the reconstruction
protocol from the drop-down menu list (Figure 5–9). Click OK to start the acquisition
Imaging Protocols
Level of Resolution Number of 2D Projections Approximate Dose
Low 360 1.2cGy
Medium 720 2.4cGy
High 1440 4.8cGy
Figure 5–9: CBCT Setup Parameters
9. The interface will display a progress bar displaying the image acquisition process
and a completion message at the end of the acquisition (Figure 5–10).
Figure 5–10: Completing CBCT
5.5.3 To Perform a FastScan CBCT

A FastScan allows the user to grab projections in 180 degrees plus the fan angle to
reduce the imaging dose by 45% compared to a 360 degree projection. This is useful for
researchers concerned about imaging dose or creating fractionated treatments.
1. First select the desired Experiment in the drop down menu or choose a New
Experiment. Then select the Cone Beam CT Menu and choose the FastScan
option.
Figure 5–11: Select FastScan
2. The CBCT parameters will look the same, but the number of projections will be set to
199. Be sure to choose the FastScan Reconstruction protocol (MouseCroppedFast).
Figure 5–12: FastScan Parameters
5.6 CBCT Reconstruction
CBCT reconstruction is performed in parallel with CBCT acquisition. While the progress
bar (see Figure 5–10) displays the image acquisition, the MuriSlice is launched and
performs reconstruction. It uses a FDK algorithm on a Tesla GPU. Many reconstruction
protocols can be made with the different filters and voxel sizes offered.
The MuriSlice Manual (Section 6) presents the steps required to perform CBCT
manipulation.
5.7 View CBCT
If the CBCT MuriSlice window does not launch automatically, View CBCT can be used to
view a CBCT scan in the MuriSlice software.
To view a CBCT scan:
1. Select the experiment via the drop-down menu in the main interface panel.
2. Click the View CBCT button (Figure 5–13) located in the CBCT acquisition area. If
there is more than one CBCT scan for the current experiment, the software will
prompt to choose the CBCT scan from a drop-down menu (Figure 5–13). It will then
ask which reconstruction protocol is desired for the specific scan chosen.
Figure 5–13: Steps to View an Available CBCT Volume
5.8 Locating the Target
When the CBCT reconstruction is complete, the target can be located in the MuriSlice
window (Figure 5–14).
The MuriSlice software is used to evaluate the CBCT, create reconstructions and define
targets or isocenters. The scan should now be displayed on the screen. To display a list
of MuriSlice keyboard short-cuts, under the Help Menu, select Getting Started.
Figure 5–14: Locating the Target in the MuriSlice Window
Note For a more complete list of MuriSlice functions, consult the About tab, Getting
Started section.
The coordinates of the target are displayed in the pixel value on the right side
window.
MuriSlice Software Options:

• Pan: ctrl + left click and drag
• Scroll through slices: wheel of mouse
• Zoom In/out: ctrl + wheel of mouse
5.8.1 To Locate a Target
1. Select Auto in the scan window (right menu) to automatically change the
contrast. Contrast can also be manually changed using the sliding bars for white
and black.
2. Select an isocenter by left clicking in a planar window at the desired target location. Verify
in all 3 planar windows that the target is properly placed. Then select Create from the List of
Reference Points (right menu) to create the Isocenter. Choose a name and click OK.
3. You will need to know which angle you want to irradiate. Measure the distance
from the surface of the specimen along the point of Radiation Entry of the target
by selecting a new target at the surface of the specimen. This can be called “Skin to
Isocenter at Gantry x”. Then select the isocenter and the newly created point at the
surface of the skin by holding down ctrl and left click both names. The distance
between the two will be just above the create button.
5.8.2 To Move to a Target Location
1. Select Accept Coordinates in the MuriSlice window (Figure 5–14) to pass on these
coordinates to the SARRP interface (Figure 5–15).
2. Click OK in the main interface (Figure 5–15) to accept coordinates as the new
isocenter goal.
3. Select Move to relocate the target to the beam isocenter (for example, ISO CT will be
equal to ISO goal).
Figure 5–15: Coordinates of the Target Received from MuriSlice
5.9 Image Confirmation
5.9.1 Simple Image Capture

Images can be captured on the Flat Panel and/or the Portal Camera without the
treatment collimator, achieving an open field view. The treatment collimator can also be
used in this type of imaging to visualize the irradiation area.
Figure 5–16: Portal Camera Image

5.9.2 Double Exposure Image Capture
An open image can be overlaid with an irradiated field of view to provide a record of the
exposure. This type of overlaid image is called a Double Exposure.
To Create a Flat Panel Double Exposure:
1. In the treatment position and with an Imaging setup in place, turn on the X-
rays.
2. On the bottom right panel Choose Capture on the Flat Panel Tab.
3. Turn X-rays off.
4. Save this image as the “Open Field” Image.
5. Place the collimator and take another image.
6. Save this image as the “Collimated Field”.
7. Open ImageJ and choose File -> Import -> Raw and open the “Open Field” image.
8. In ImageJ again import a raw image and choose the “Collimated Field” image.
9. In ImageJ, Choose Image -> Overlay -> Add Image. You will have one image
selected (either Open or Collimated) and choose the other image in the drop down
box. Change the Opacity to 70% and select OK.
Figure 5–17: Portal Camera Double Exposure Image
This same process can be completed with the Portal Camera. Pull the Portal Camera out
of its housing in the Gantry with the black finger pull. The Portal Camera offers images
from a Beam’s Eye View.
5.10 Irradiation Delivery
SARRP has multiple methods of delivery:
Methods of Irradiation Delivery
Conformal Arc Conformal arc therapy is possible with SARRP. The X and Y
Therapy (Conventional coordinates of the robot are continuously adjusted to keep the target
and Conical) at the isocenter. Radiation from either the Theta or Gantry angles
can be performed by use of the Continuous Arc Motion menu.
Direct Radiation Using Beams, the coordinates of the target are read by the software
(Beams) from the selection using the CBCT image. After selecting the Theta
and Gantry angles for the beam, the user selects Move in the SARRP
Software to setup for an irradiation.
The Delivery sub-menu has a Dose Calculator designed to calculate the exposure time
based on the radiation parameters specified by the user.
These parameters include collimator size, source-to-surface distance (SSD), dose depth
and desired dose (Figure 5–18). After a calculation is complete, Apply Setting enables the
user to send the kV, mA and exposure time to the X-Ray control software.
Figure 5–18: SARRP Dose Calculator
Note: Due to the difficulty of finding a constant depth in an arc, it is recommended to calculate dose for
an arc utilizing MuriPlan.
5.10.1 To Setup for an Irradiation

1. Change the filter to the copper filter and put the flat panel shield in place.
2. Select a preset or set the parameters on the controller (MP1). Check broad focus,
220 kV, 13.0 mA and enter the exposure time.
5.10.2 To Irradiate following CBCT guidance with a Beam
1. Select Dose Calculator from the Delivery sub-menu (the main interface toolbar)
(Figure 5–18).
2. Enter the Collimator, SSD (Source to Skin Distance), Depth (in tissue) and Dose.
3. Choose Calculate.
4. When Apply Setting is chosen, the kV, mA, Broad Focus and Exposure Time are
automatically sent to the X-ray control Software.
5. Ensure the subject has been moved to the chosen Isocenter. Move the Gantry to
the chosen Treatment Direction.
7. Press X-rays on to complete the treatment.
Figure 5–19: Irradiation with Dose Calculator Setup
5.10.3 To Irradiate following CBCT guidance using an Arc:
Note: This is recommended only with the use of MuriPlan due to the its accurate
dose calculations.
1. Ensure the subject has been moved to the chosen Isocenter.
3. Select Continuous Arc Motion from the Delivery sub menu (the main interface
toolbar).
4. Enter the Gantry Start and Stop angles for a Conventional Arc Treatment. For a
Conical Arc treatment, verify the Gantry is not at 0 degrees and both Start and Stop
are the same. Change the Couch Start and Stop angles. Choose to either enter the
time or the speed and the other will automatically fill in.
Figure 5–20: Continuous Arc Motion
5. When you choose Perform Arc Motion, the Gantry or couch will automatically move
to the Start Location. If the motors are stopped by the user during setup, then the
Arc Motion needs to be exited and started over.
6. When the SARRP software alerts of X-Rays imminent, press OK when ready.
Figure 5–21: ARC X-Ray On
5.11 BBQA Procedure
To conduct a BBQA procedure:
Figure 5–22: QA Block with a BB on top
1. Conduct a CBCT with a BB embedded in the QA block
2. Use the MuriSlice software to zoom in on the BB for the best accuracy. Target the BB in the
on the CBCT and create an Isocenter. Select the Isocenter, Choose Accept Coordinates and
Move the stage in the SARRP Control Interface.
3. Verify Laser alignment in the spaces on the QA block.
4. Complete a Double Exposure with the Flat Panel.
5. Verify that the BB is seen in the 5mm x 5mm collimator window.
6. The Double Exposure should be saved and dated as part of an ongoing QA process.
5.12 Power Down SARRP
1. Return the platform to origin (X:0mm, Y:0mm, Z:0mm, stage 0º and

Gantry 0º) and remove the collimator.
2. Remove all Small Animal Beds.
3. Ensure the Detector Shield is Pulled down into its home position.
4. Shut the SARRP Door.
5. Turn the Software and Computer off.
6. Turn the MP1 Key to Standby (Position 2)
7. Depress the STOP button on the SARRP.
8. Turn MP1 Key to OFF, remove and store in a secure location.
CAUTION: After every final irradiation, ensure the SARRP is left on

for 10 minutes prior to turning the power off to allow enough time to
cool down the SARRP.

Section 6:
MuriSlice® Manual
in this section
6.1 MuriSlice Overview ...................................................................................... 1
6.2 Volume Visualisation: DigiOBS Module ....................................................... 4
6.3 Operator Functions .................................................................................... 11
6.4 Tomographic Reconstruction ..................................................................... 19
6.5 Analysis of Cutting Planes: DigiCUT Plug-In ............................................. 41
6.6 Automation of Reconstruction Tasks: Batch Mode .................................... 49
6 MuriSlice® Manual
6.1 MuriSlice Overview
MuriSlice® is a software solution by Digisens® Company. This section is provided

courtesy of Digisens. The reproduction, transfer, distribution or storage of part of or
all of the contents of this document in any form whatsoever is forbidden without the
prior written permission of Xstrahl and Digisens.
MuriSlice software enables the SARRP user to:

• Calibrate CBCT geometry
• Reconstruct CBCT acquisitions
• Visualise volumes and meshes
• Manipulate 3D cutting planes and
• Take basic measurements
MuriSlice software has two main modules and ten processing plug-ins:
MuriSlice Main Modules and Processing Plug-Ins

Main Modules DigiOBSa Visualisation and 3D analysis software
DigiR3D 3D Reconstruction on multiple GPU’s
Xstrahl SARRP Operator Manual Section 6: MuriSlice® Manual
MuriSlice Main Modules and Processing Plug-Ins

Processing DigiCUT Analysis of cutting plane and
Plug-Ins measurements
DigiSRF Extraction and mesh visualisation
DigiSIM Import of slices
DigiCAL Reading acquisition geometry
DigiFDK Feldkamp analytical algorithm
DigiSNP Snap CT GPU acceleration
Batch Module for producing macros by

Mode command line
a. Main modules and plug-ins are brought together in the same

interface based on the DigiOBS module.
6.1.1 Minimum Configuration Requirements
Minimum recommended configuration for a desktop computer:

• Double slot PCIe motherboard
• Intel quad core processor
• 12 GB RAM minimum (two times the total amount of GPU RAM)
• Windows XP/Windows 7 64-bits
• 10000 rpm hard disks, mounted as RAID 0 drive or solid state drive (SSD)
• NVIDIA Fermi board dedicated to computation (Tesla board)
• NVIDIA board for visualisation
Minimum recommended configuration for a laptop computer:

• Intel dual core processor
• 4 GB RAM
• Windows XP/Windows 7 64-bits
• High speed hard disk
• Quadro 2000M graphic board
• No IGP enabled
• Optimus technology disabled
Section 6: MuriSlice® Manual Xstrahl SARRP Operator Manual
6.1.2 Installation
The installation of MuriSlice begins from the execution of the file
MuriSlice_X_XX_X.exe (where X_XX_X corresponds to the installer version tag).
Once the installer has started, follow the installation wizard.
For help with installing or launching the application, contact Xstrahl Technical
Support.
6.1.3 Diagnostic Window
After launching the application, if the graphic configuration is not adapted, a

diagnostic window appears (see Figure 6–1:). This window displays the graphics
card reference, the OpenGL version, the OpenGL extensions required, and whether
any extensions are missing.
In the event of display issues, this information should be given to the technical
support.
Figure 6–1: Graphics Extension Report Window
6.2 Volume Visualisation: DigiOBS Module
DigiOBS module corresponds to the main GUI of Digisens’ product. It allows the
visualisation of datasets and provides all necessary links between the visualisation
and product features.
Maximum resolution depends on the capacity of your workstation. This

documentation refers to standard resolution of 512 x 512 x 512 voxels.
6.2.1 Presentation of the Default GUI
MuriSlice appears in the form of a main window (see Figure 6–2:) made up of a 3D
visualisation area, a menu and a tool bar. The tool bar contains short cuts to the
main functions and parameterisation dialogue boxes.
Figure 6–2: MuriSlice Main Window
6.2.2 Management of Preferences
An advanced user can define his environment and a certain number of other
parameters via the DigiOBS preferences. In order to define parameters, the
preference window must be opened (see Figure 6–3:).
To open preferences:
 Select File then Preferences
Preference Window Tabs

Computation Parameters useful for tomography reconstruction
Interface User interface colour parameters, management of

windows and multi-display configuration
Graphics Display parameters
Figure 6–3: Opening the Preferences Window
6.2.2.1 Computation Tab

This tab has two fields used for reconstruction. These parameters are used by
DigiR3D plug-in (CPU Reconstruction and GPU Reconstruction), see Figure 6–4:
Figure 6–4: Preferences Window Computation Tab
Figure 6–5: Computation Thread Number
The number of threads for computation corresponds to the number of processes that
can be launched in parallel onto the CPU. It depends on the workstation’s architecture
and more specifically, on the total amount of cores in processors. The preferred
memory size for the calculation of a sub-grid corresponds to the maximum memory
which can be allocated for the calculation. This value depends on the amount of
RAM memory available on the computer. It corresponds to the remaining memory once
all of the system processes have been launched.
Figure 6–6: GPU Reconstruction Check Box
6.2.2.2 Interface Tab

MuriSlice has a tool for informative measurements (see DigiCUT plug-in). In order to
adapt to the system of units of one’s country, measures can be converted in
millimetres (international system of units) or imperial units (for example, inches,
millimetres).
Figure 6–7: Converting Measurement Units
Note This change in units is not applicable to tomography geometry definition, which will remain in
the international system of units (millimetres).
Using this interface (see Figure 6–9:), the user can change the background colours of
DigiOBS. A plain background colour can be used in both Background Color Up and
Background Colour Down, or gradients of colour can be used.
Figure 6–8: Colour and Texture Options
The Textured Option allows an image to be used as wallpaper for DigiOBS.

Compatible formats are jpg, bmp or png. This image replaces colours defined in Color
Up and Color Down. The option, Selected Color corresponds to the colour of the
elements selected in the 3D grid and Outline Color to the colour of the physical limits of
the visualised 3D volume.
The user can also change the icon sizes by selecting Icon Size from among the four
available formats.
Figure 6–9: Interface Tab
The Multi-Display Configuration allows the parameterisation of multi-display. The

Display Plane Names box allows the X, Y, Z slices plane to be renamed in the GUI as
Sagittal, Transversal and Coronal views. Be default, these names are Front, Side and
Top. Draw Lines in Single Display allows the tracing of the edges of the planes
intersecting the active display in the visualisation.
The Automatically Dock Window at Startup box allows the analysis window to be
integrated into the main MuriSlice window, as shown in (Figure 6–10: and Figure 6–11:).
Figure 6–10: Marker Tool Docked in Interface
Figure 6–11: Marker Tool Not Docked in Interface
Default configuration corresponds to docked windows.
To dock a window:
Double click on the upper bar of the window or drag it to the edge of the main
window.
To undock a window:
Either tick the Automatically Dock Window at Startup box in preferences, or left click
the window banner (while keeping the button pressed) and drag the window to the
middle of the main DigiOBS window.
6.2.2.3 Graphics Tab

DigiOBS offers a powerful and realistic 3D rendering tool.
To enable the 3D rendering tool:
Select the Volume Render check box feature (see Figure 6–12:)
Figure 6–12: Graphics Tab
Graphics Tab Options

FAILSAFE Allows all of the openGL options to be invalidated. The final rendering
Opaque Volume is very poor; compatible with any graphic card.
Disable Volume Deactivation of 3D rendering mode by ray tracing method. Only

Render recommended for graphic cards with performance equal to or better
than NVIDIA 8800/8600 cards.
Fragment Shared texture and palette extension, palette texture extension, pixel
Program map, colour table, colour matrix, texture 3D: increasingly slower and
decreasingly powerful display mode.
Force Max Current graphics cards know how to manage 256 or 512, depending
Texture Size to on the type of card
6.2.2.4 DigiXST Tab

By default, set the parameters as illustrated in Figure 6–13:. The orientation may
need adjusting based on the specific SARRP hardware configuration.
Figure 6–13: Parameters
6.3 Operator Functions
6.3.1 Loading a Volume
To load a volume:
1. Select View CBCT button in the SARRP GUI

2. Select the *.xst folder in C:\CBCT_Data\Experiment\Scan\... by left + clicking the
folder while holding down the mouse and dragging the cursor into the application
window, then releasing the mouse (see Figure 6–14:).
The loaded volume file’s name appears in the window title (see Figure 6–15:). To
manipulate the volume, use the mouse and keyboard.
Note For optimal navigation in DigiOBS GUI, use a mouse with a roller wheel.
Figure 6–14: Opening a Volume File
8/9/14 All rights reserved.
Figure 6–15: Visualisation of Turbine Blades
6.3.2 Volume Visualisation
6.3.2.1 Multi-Display Visualisation

DigiOBS offers simultaneous display of the 3D Rendered Object and 3 Cutting
Planes.
Six display modes are available using the menu or button switch mode:
Display Modes
3D Display
3x1 Display
2x2 Display
Side Display
Top Display
Front Display
Switch Modea
a. Switch mode allows modes to be changed (1 x 1).
Figure 6–16: Example of 3-to-1 Window Mode Visualisation
6.3.3 Managing a Volume
6.3.3.1 Display Management
Using the Mouse

The mouse can be used to navigate around the volume object (see Figure 6–17:).
There are two modes of moving: one for moving the volume and one for moving the
cutting plane. Pressing the Mouse Control Mode button or alternatively, depressing the
space bar on the keyboard enables the switching between these two modes.
The 3D Volume icon becomes Cutting Plane mode. Manipulating the

mouse in the same manner as moving the volume will move the cutting plane. See
Figure 6–18: for an example of a cutting plane.
The left mouse button will enable the cutting plane to turn. the right button enables
translation on the plane and the roller wheel allows for perpendicular translation to the
plane. Keyboard keystrokes can also be used and are shown in Figure 6–19:.
Figure 6–17: Using the Mouse to Manipulate 3D Volumes
Figure 6–18: Using the Cutting Plane
Figure 6–19: Active Key Strokes
6.3.3.2 Volume Alignment

Displayed volumes are expressed in a separate reference axis—the centre of which
coincides with the centre of rotation of the system. This reference axis is called World
Reference (see Figure 6–20:) and can be activated by using the keyboard shortcut “a”.
It is used to determine the centre and orientation of a section extracted from the volume.
DigiOBS uses two other reference frames:

• A reference frame in relation to the region of interest described in the
DigiR3D section and named volume reference (See Figure 6–20:).
• A reference frame for measures, enabling them to be expressed in regards to an
alignment which can be in relation to a CAD model (measure reference in Figure
6–20:)
The user can align the volume by moving and/or rotating the measure reference. This
feature is useful in measure mode because it allows for expressing the location of an
entity with regard to an absolute reference (for example, a CAD reference).
To enable volume alignment mode:
Click on the button. When the button becomes yellow , the mode is
active. Fields will appear at the bottom of the GUI (see Figure 6–21:)
Note: The mode may be unadapted with other mode functionalities of MuriSlice.
In this situation the button will be greyed.
Figure 6–20: Reference Axis Definition in MuriSlice
During the alignment process, the former orientation of the volume remains
displayed with dashed lines.
The new reference is defined by:

• Cutting planes axis red, green and blue
• Intersection of those three planes
Figure 6–21: Volume Alignment
To fix the volume orientation:
1. Click the Lock button at the bottom of the GUI to move the volume.
2. Click Lock again to validate the orientation once the orientation has been
fixed.
To fix the origin of the new reference axis:
Locate the origin by navigating the three 2-dimensional views on the left of the
GUI in Figure 6–21: and click the Set button. The origin corresponds to the
intersection of the three planes.
When everything is complete, all measures described in the DigiCUT chapter will be
expressed according to this reference axis set.
6.3.4 Data Management
6.3.4.1 Saving and Exporting Volumes

The Save Volume menu enables the operator to save volumes and is directly enabled
by selecting File Export, then Volumes and Slices. The currently displayed volume (for
example, dimensions, resolution, display LUT, etc.) is saved.
The available formats for saving are a proprietary format (*.vol) and two other formats
providing compatibility with third party analysis software (for example, Visilog im6 and
Volume Graphics vgi formats). In order to save the volumes in another configuration,
the user must use the Export Volume menu.
The menu allows the displayed volume to be exported through modification of some of
the parameters:
• Volume dimensions (see Figure 6–22:); by clicking Resize the final

dimension of the output volume can be selected.
Figure 6–22: Modification of Data Dimensions
6.3.4.2 Screen Dumps

To perform a screen dump of the current display:
1. Select Window then Export Image

2. Select the directory, the name of the file to be saved and the file format (jpg, png,
eps, ps, ppm, bmp and fig)
This function can also be activated via the button
Figure 6–23: Example 1: Mouse
Figure 6–24: Example 2: Mouse Inferior to Superior
Figure 6–25: Example 3: Superior to Inferior
Figure 6–26: Example 4: Anterior to Posterior
6.4 Tomographic Reconstruction
6.4.1 Introduction
DigiR3D is the tomography reconstruction module of the MuriSlice software suite. It

produces the cartography of the attenuation of an object based on a stack of X-Ray
projections acquired from several different angles.
DigiR3D commands are accessible from the Tools menu (Tools then 3D
Reconstruction Parameters) or toolbar (see Figure 6–27:). This command opens the
acquisition geometry configuration and reconstruction parameters dialogue box and
launches the reconstruction of the volume.
Figure 6–27: FDK Configuration Icon on Toolbar
6.4.2 Workflow Definition
Figure 6–28: illustrates the DigiR3D GUI docked into the main DigiOBS window.
DigiR3D consists of five ordered toolboxes:

• Hardware Definition
• Input
• Output
• Reconstruction
• Preview/Adjustment
Organising the workflow in the above order provides a clear vertical workflow for the
user.
Each toolbox has at least one tab corresponding to one mandatory group box, as well as
additional features enabled from export mode or license. These tabs provide tools for
specific applications, such as phase contrast tomography, or features helping to
reconstruct datasets (calibration tool). They also provide access to image processing
tools and iterative algorithms.
Note See the X-Ray CT System Compatibility section for how to use DigiR3D with the X-Ray
manufacturer system geometry file.
Figure 6–28: DigiR3D Main Window
6.4.3 Hardware Definition Toolbox
The Hardware Definition toolbox describes the user’s CT hardware.
6.4.3.1 Camera Definition Tab (Mandatory)

The Camera Definition tab is where the user describes the imaging sensor used.
Several scenarios are possible:

• If DigiR3D is being used for the first time, the GUI requests the user create a camera
(see Figure 6–29:)
• If the camera definition has not been created, the software automatically finds
the correct camera definition and enters this in the correct field.
• If several cameras are compatible with the currently loaded dataset, a popup will
appear requesting the correct camera definition.
• If a camera does not exist, the field will be set to create camera. The user will
have to create a camera definition.
Figure 6–29: Camera Definition Tab
Enables a new sensor to be added
Removes imaging sensor
Figure 6–30: shows the camera creation window. The user must assign the
camera a name, resolution in pixels and size (in pixels). The camera size fields
will automatically be entered once this information has been provided.
6—22 8/9/14 FMSARRP E ©2014 Gulmay Medical Inc. (an Xstrahl Company).
Figure 6–30: Create a New Camera
Specific applications require acquisitions of objects larger than the field of view, so the
system is equipped with a shifted detector, as illustrated in Figure 6–31: and Figure 6–
32:. The mandatory condition to perform a good reconstruction with this acquisition
setup is to maintain an overlapping area between views of at least one third the size of
the detector width.
When the definition is correct, clicking the Create button will return the user to the main
interface screen.
Note Figure 7-51 illustrates a standard geometry where the orthogonal ray from
source to detector hits the detector centre (SOD is the source of the object
distance, SDD the focaldistance and Umax the detector width).
Figure 6–31: Extended View Mode: Standard Geometry
Figure 6–32: Extended View Mode: Shifted Detector
6.4.3.2 Geometry Calibration

MuriSlice provides a calibration tool to determine the required parameters in
achieving a good tomographic reconstruction (rotation centre, focal length, etc.) based
on the capture of some radiographic acquisitions from a calibration test pattern. This
test pattern is provided by Xstrahl. This feature is license protected.
6.4.3.2.1 Calibration Procedure
Required calibration procedures for tomographic scans:

• X-Ray acquisition of an object is carried out in the tomography system. The scan
consists of a predefined number of images taken under different angles (or
views).
• A test pattern, size compatible with the previously scanned object has to be
acquired using the same system setup. A fast recording is carried out with a
complete rotation and a reduced number of images (minimum of 60 projections
and always a multiple of 4).
• The calibration plug-in estimates the geometry of the system based on the
processing of a previously acquired calibration dataset. At the end of the
process, the user exports the calibration results in a *.cal file.
• The software will generate a 3D reconstruction of the scanned object, ready for
visualisation and further analysis.
Figure 6–33: Detector Location Illustration
Rules for Good Results

Geometric settings of the CT system must not be changed between stages 1
and 2 (for example, the position of the tray, the source and the detector must
be maintained). Because of the mechanical tolerances of the robotics, the
robotic arm never returns to the requested position, even if the accuracy of the
positioning sensor is close to one micron.
If the object to be reconstructed is heavy, it is recommended to put in a tare of

approximately the same weight to compensate for the effects of robotic
buckling. The buckling implies variations in the position of the rotation axis of
several microns.
Rules for Good Results

Stages 1 and 2 can be executed in a different order. An entire series of objects
can be scanned using the same calibration, but it is recommended the user
does calibrations at the start and end of the acquisition series to ensure the
machine has not shifted or been accidentally adjusted.
At least 5 spots must be chosen, but 10 are recommended. They must be at

least one diameter away from the edge of the image and remain so during the
complete revolution.
6.4.3.2.2 Calibration GUI and Steps for Calibration

To go to the calibration interface:
 Click the Geometry Calibration tab (see Figure 6–34:)

Figure 6–34: Calibration Geometry Tab
To perform calibration:
1. Select Choose Input Image from the toolbar shortcut to load the images to
calibrate (Figure 6–35:). All images of a similar name (base name without image
number) will be selected.
Figure 6–35: Image Loading for Geometry Calibration
2. Use the Probe tool to define the size of the probe, the relative position and
number of spots (see Figure 6–36:).
Figure 6–36: Probe Definition
3. Indicate the dimensions of the spots in the Initial Search Size field by clicking
on the image of a spot to launch the automatic search of its center and radius.
Clicking on an already selected spot deselects it; double clicking deselects all of
the spots.
Note The spots must be selected in order (preferably from the highest to the lowest on
the screen) and never in a disordered manner. The selected spots must be visible
in all of the images and must never be partially hidden or cut off.
In order for the trajectory of the probe spots to be monitored correctly, the initial
speed (in the image plane) of the spots must be low (for example, start the spots
positioned completely on the left or the right of the image). To reach this position,
use the cursor below the image. The initial position of the probe must be defined in
this image.
The probe can be validated by clicking the short cut, Set probe, and by returning the
distance between the centre of the first and last spot of the probe or by clicking on
the button Guess Probe, if a calibrated probe is used.
When calibrated probes from Digisens are used and when beads are clicked, clicking
on Guess Probe will automatically identify the probe and define the distance
between the upper and lower spot.
The accuracy of probe size can be found in all distance measurements of

reconstructed volumes: an overestimation of 1% (160 microns in our example) in the
probe results in an overestimation of 1% on all size measurements of the
reconstituted object.
Figure 6–37: Spot Selection
Recommendations:
• A standard toolset of two probes; one equipped with 0.4 mm diameter beads
spaced by 1.4 mm and the second, equipped with 2 mm diameter beads
spaced by 5 mm.
• An optional recommendation are calibrated probes accompanied by a
metrology inspection report (see Figure 6–38:). The probe and the report are
unique. The probes have two advantages; the tomography system is linked to
metrology national references and provide a simple tool for system calibration
follow-up. The design is unique and thus, the calibration tool is able to
automatically detect spots and provide the user with the right probe size using
the Guess Probe button. Using these probes provide a calibration repeatability
lesser than 5 μm, whatever the system focal and user settings.
Figure 6–38: Calibrated Probes
4. The Region of Interest section (red and green borders, see Figure 6–39:)
enables the image to be cropped. This is rarely useful, other than when spots get
too close to an image border leading to a tracking failure. The uMin, uMax values
therefore represent the horizontal interval used and vMin, VMax, the vertical
level used. It is also possible to fix the focal distance value in advance to improve
the geometry estimation accuracy.
5. Once the probe has been specified, the Compute button allows the calibration
calculation to be launched. The calculation can fail (red marking on one or several
spots) for the following reasons:
• The initial speed of the spots is too high: the processing must be started on
an image where the spots are completely on the left or on the right of the
field of view.
• The speed is not regular: an image must have jumped or been
processed twice. The calibration sensing procedure must be revisited in such
a way as to have regularly spaced out images.
• A spot collides with the edge, and the automatic search detects a sharp
variation in spot diameter. The parameters uMin, uMax, vMin or vMax must
be used to trim the images, or this spot should not be selected for the
calculation.
• In a particular angle (or in a certain part of the sensor), the probe

support is too contrasted which prevents the spots from being properly
detected. The contrast setting must be re-visited.
• The most horizontal trajectories tend to introduce greater centering
errors. The (one or two) spot(s) nearest the center of the image should be
deselected.
• A spot can shift in the probe during sensing. In this case, the trajectory will
be badly centered. It should not be selected in the probe.
When the calculation is successfully completed, the calibration tool posts a results
table and spot trajectory is displayed (see Figure 6–37:).
Figure 6–39: Calibration Result Example
The programme cannot find a solution with less than 3 spots. At least 5 or 6 are
necessary to generate error calculation results. However, 10 or so covering the whole
of the area to be reconstructed would seem to be optimal.
6.4.4 Input
The Input Toolbox aims to describe and to process projections used to achieve a
correct reconstruction.
6.4.4.1 Input Definition (Mandatory)

The Input Files field (see Figure 6–41:) indicates the directory where the projections
are located (can also be selected using Explorer by clicking the “...” button. Image
formats supported are TIF, DICOM, VFF, ATN, RAW, JPG and BMP.
Figure 6–40: Input Tab Presentation
Figure 6–41: Input Files
With regards to acquired image type, several scenarios should be considered:

• (General Users of SARRP) Select the Set White Level radio button, then
Compute.
• If images are intensity-based, use a flat field image (for example, bright image,
beam profile image, etc.). To inverse the Beer Lambert Law (using the
image), select the image using Explorer by clicking on the “...” button. The
software will automatically compute an attenuation image by dividing the flat
field image by the acquired projection, and also by computing the logarithm of
the resulting image.
• If the flat field image does not exist, generate a constant image with a level
corresponding to the mean value of the bright image. This level can be
measured on a small region of interest where the object is not present; or
alternatively, use the mean value of the entire image stack. If this measure is
impossible, set a 0 value in the Set White Level field.
Once the images are loaded, the next step is to indicate the angular range. This is
completed by filling in the Angles Definition field. MuriSlice can manage both full scan
acquisitions (angular range of 360º) or partial scan acquisitions (at least 180º + beam
divergence). Any value can be entered in this editable field (Figure 6–42:).
Figure 6–42: Angles Definition
Corrections can be made to images. Selecting both the Expert User check box
and the corresponding image will compensate the images from electron noise
offset (see Figure 6–43:).
Use Defect Map eliminates pixels or pixel clusters with an abnormal response
with null or saturating response, whatever signal is received. In a tomography
field application, this correction is mandatory to remove the well-known ring
artifact. The image used for this processing must be binary: white level for
abnormal pixels and black level elsewhere.
Figure 6–43: Additional Image Correction
Note The projections are displayed as they will be used in the Reconstruction step.
This means the projections background should be dark and the part brighter.
6.4.5 Output Definition (Mandatory)
6.4.5.1 Volume Format and Name
Two formats are handled by MuriSlice:

• Image Stack Format (format V0 with extensions TIF, RAW, DICOM, JPG,
BMP, etc.)
• MuriSlice 3D file format (volume V2)
Figure 6–44: Projections Registration
To define the name and location to save the reconstruction file:
1. Click the “...” button to open a file browser and save the information. Create a
new folder ending with “.xst” in the scan directory.
2. Set File Name, Volume and Save As type: Dicom image
6.4.5.2 Volume Dimensions to be Reconstructed

The Dimension field allows the name of the file containing the reconstruction data
and the directory in which they will be stored to be specified. The volume dimensions
(in mm) are defined by the centre of the 3D grid to reconstruct (Center) and the size
of the grid (Size) shown in red. These two values can be automatically positioned
(auto box) in order to reconstruct an optimal volume in relation to the data supplied, or
they can even be adjusted manually in order to only reconstruct a chosen zone.
Figure 6–45: 3D Reconstructed Volume Definition
Note We can intuitively expect that default dimensions proposed by the software have
the resolution of the detector in width and height. Figure 6–46: illustrates the
estimation of the dimensions. In a conical context, the reconstruction will be made in
the cylinder registered in the cone of the beam as defined by the dimensions of the
detector. The reconstruction grid contains this cylinder. The figure shows that in a
general conical case, the cube is narrower here than what it would be if the beam
divergence was weaker because the inscribed circle has a diameter smaller than in a
situation where the beam divergence is weak.
Figure 6–46: Determination of Reconstruction Grid Dimensions
6.4.5.3 Region of Interest

A region of interest can be reconstructed in volume (see Figure 6–47:). This is
completed by either returning the dimensions of the area of interest using the
MuriSlice interface or by using the multi-display visualisation described in section
6.3.2 and defining the area of interest using the mouse. In the latter case, the Define
ROI for Reconstruction box must be checked.
To visualise the reconstruction:
 Select Show Preview, then 3D at the bottom of the panel

The dimensions of the region can simply be changed by left + clicking
the boundaries, while holding the button down and gently dragging to adjust
the boundaries. The 3D visualisation window (which defines the volume) is
then updated. In order to refine the definition of the area of interest, zoom in by
pressing the control button and using the mouse’s wheel. To return to the original
zoom, press the keyboard’s control button and left + double click the mouse.
Figure 6–47: Definition of the Reconstruction Area of Interest
6.4.5.4 Volume Resolution

The resolution of the volume for each of its dimensions is demonstrated in (see
Figure 6–48:). The resolution of the reconstruction can be directly set either by
clicking on the buttons corresponding to a pre-defined resolution value, or by
choosing Other, which enables a value to be put in whatever the resolution. Once the
resolution has been chosen, object dimensions in voxels are updated.
If an ROI has been defined for reconstruction, select Best, otherwise select Other and
set a voxel size of 0.25 mm.
The resolution of the volume in each of the dimensions is indicated (see Figure 6–
48:), so reconstructed voxels are not necessarily of the same size on the three axis.
Figure 6–48: Volume Resolution
6.4.5.5 Cylindrical Reconstruction Constraint

The cylindrical constraint allows limiting the reconstruction of a region of the space
corresponding to the intersection of the back-projection of all the available
projections. This intersection is centred on the axis of rotation. Outside, the data
corresponds only to the intersection of some beam rays common to some projections.
They are thus carriers of information with a weaker signal to noise ratio. The
information is thus degraded by a stronger noise and the levels of density can be
biased. Figure 6–49: illustrates the effect of the cylindrical constraint.
If the subject is well centred with the axis of rotation, enable the cylindrical
constraint.
Figure 6–49: Effects of the Cylindrical Constraint of Reconstruction (Top) Without

Cylindrical Constraint (Bottom) With Cylindrical Constraint
(Top)
(Bottom)
6.4.6 Reconstruction Grid Orientation
Using expert mode, it is possible to rotate the volume according to an orientation

chosen during the preview step (see Figure 6–50:). As demonstrated in section 6.3.3,
several axis references are used in the software. The modification of the quaternion
acts directly on the volume reference.
To modify the orientation of the object:
 Fix the axis of rotation and the value of the angle of rotation.
Figure 6–50: Rotation Grid Definition
During modification of the grid rotation parameters, an overlapping box is added in

which the volume preview is visible. This additional box illustrates the rotation which
will be applied to the reconstruction grid with regard to the original reference.
6.4.7 Reconstruction
MuriSlice software allows you to select reconstruction algorithms based on the

geometry of the acquisition system or scan set up. The standard reconstruction
method for SARRP acquisitions is FDK.
6.4.7.1 Filtered Back Projection

Filtered back projection is the most recognised approach in tomography
reconstruction. Its ease of use and speed make it a reference in the field of application
and its approach is a member of analytical reconstruction methods.
FDK or FBP need the filtering projections by the mean of a ramp filter, defined in the
frequency domain. The main drawback of the ramp filter is that it amplifies noise as it
restores object resolution. In order to reduce noise degradation in reconstructed
volume, an aposidation filter is combined to ramp filter. Its aim is to reduce or
eliminate high frequencies in the image (noise). Unfortunately, high frequencies are
necessary to restore the object resolution. Hence, filtering projections is a balance
between signal to noise ratio and resolution. That is why the reconstruction module
proposes several aposidation filters, each one making its own balance: ramp filter for
high resolution reconstruction, but with lower signal to noise ratio than a combination
of a ramp filter and a Welch filter, which increases signal to noise ratio but reduces
resolution.
The following shows the shape of combined filters in Fourier space. Hence, it can be
seen that the spare filter (ramp filter without aposidation) restores resolution
regardless to signal to noise ratio. The opposite Welch filter, combined with the ramp
filter increases signal to noise ratio, regardless of resolution. Using those aposidation
filters leads the user to accept a trade-off between noise level and resolution.
Figure 6–51: Reconstruction Filter Comparison
Figure 6–52: Examples of Aposidation Effects Regarding Noise Level and

Reconstruction Resolution
6.4.7.2 Post-Processing
The user can apply to the reconstructed volume 3D post-processing to improve
image quality by selecting Expert User.
6.4.7.2.1 Ring Artifacts Remover

Ring artifacts have several origins, all of which are connected to an incoherence of
pixel behaviour with radiation, for example, dead pixels or pixels with the variability of
their response to illumination with regard to the others. In the latter example the
incoherence between the flat field image and the acquisition can be at the origin of
ring artifact in the reconstruction. Several approaches exist to correct these pixels.
Several tools are proposed in pre-processing of the projections or the sinogram itself.
The tool proposed here is applied to the reconstructed volume. The principle is based
on the detection of rings and their deletion.
Both accessible parameters in expert mode are the maximal thickness of rings to be
deleted (size), and Alpha, which takes into account if rings are complete, constant or
modulated (for example, partial rings). By default, parameter value is 3 for size and
0.2 for Alpha.
Figure 6–53: Ring Artifact Reduction (Left) Raw Image with Ring Artifacts,
(Right) Filtered Image
Note Ring artifact filter works only if the object is in its natural orientation (vertical axis
by default merged with the axis of rotation). If the orientation is used to rotate the
object after the reconstruction, this filtering is not functional. The user will be
warned by a screen message. If however, the rotation is compulsory, it will be
possible after reconstruction to rotate the object by using the reference axis
modification, as described in section 6.3.3.2.
Note Ring artifact filter is not available in slice preview mode.
6.4.7.2.2 Bilateral Filter

Bilateral filter is an edge-preserving noise reducer. In homogenous regions, a
Gaussian kernel is used to smooth pixel intensity in a range defined by kernel size.
Weighting function is composed of two Gaussian kernels:

• The first kernel is based on distance from the processed pixel, as defined by
its standard deviation σxyz
• The second kernel is based on pixel intensity, describing intensity gap

defining edges. The kernel is defined by its standard deviation σg.
Figure 6–54: illustrates how the filter works—the left image shows the signal to
process, the middle image shows the kernel shape and the right image shows
the resulting processed signal.
Figure 6–54: Kernel Definition
To use the bilateral filter:
 Check the bilateral check box and adjust the two filter parameters (one for
intensity and one for spatial characteristics (see Figure 6–55:).
Figure 6–55: Bilateral Filter Parameters
Note The above parameters are not absolute values; Sg corresponds to intensity standard
deviation relative to the min-max range of grey levels in the reconstruction. Its max value is
consequently 1. This is the same for Sxyz, but regarding volume resolution.
The implementation of this filter is fast, but the speed is in straight relation with the
parameters’ value.
Figure 6–56: Effects of Bilateral Filter (Reconstructed Slice of a Granite Sample)
6.4.7.2.3 Sharpness Filter

In tomography application, system resolution is usually degraded by focus spot finite
size, detector pixels and scintillator, and reconstruction algorithm. This degradation
can be seen as a blurring kernel, smoothing reconstruction edges after the
reconstruction process. To avoid this degradation, a filter will retrieve sharp edges.
To use the sharpness filter:
1. Select the Sharpness filter check box.

2. Enter the 3 filter parameters:
2.1. The number of iterations used for processing
2.2. The radius corresponding to a low pass filtering necessary to make filtering
stable
2.3. A speed parameter corresponding to a discretization step. If the value is
decreased, filtering is slower but finer.
Figure 6–57: Sharpness Filter Parameters
Figure 6–58: Effects of Sharpness Filter (Reconstructed Slice of a Granite Sample)
6.4.8 Preview and Adjustment
6.4.8.1 Preview Settings

Preview reconstruction allows the parameters entered in previous steps to be quickly
checked and, possibly, to be adjusted iteratively (for example, adjusting the
trajectory definition, or even, the dimensions of the volume to be reconstructed).
MuriSlice proposes two preview modes:
• Reconstruction of the whole 3D object in low resolution

• Reconstruction of a single high resolution slice, which is arbitrarily placed
due to the cutting pane.
The two modes pre-calculate a sub-collection of the low-resolution filtered
projections in low resolution to accelerate the successive previews—this
sub-collection is referred to as cache.
Images for Preview (dialogue box) can be used to modify the number of projections
used as well as their resolutions (by default adapted to the size of the low resolution
volume). The limit preventing the use of the projections in full resolution is the
memory used by the cache, which is displayed as memory used.
Low Resolution Volume Preview is accessible whichever tab is displayed at the

bottom of the dialogue box.
To launch the reconstruction:
 Select the button. This reconstructs the corresponding volume in a few

seconds. By default, three resolutions are offered: 1283, 2563 and 500e (see
Figure 6–59:).
Figure 6–59: Preview Parameters
It is possible to quickly check the coherence of the entered parameters and adjust the
volume reconstructed on a possible area of interest.
Note The user can manually enter a reconstruction resolution, for example, 32 x 128 x 64. However, as
the reconstructed volume is only destined for 3D display, we recommend the user follow restrictions imposed by
the graphics cards used. The resolutions should be a power of two and for most graphics cards; the 3D
display resolution is limited to 512. Not following these restrictions does not involve an error, but causes re-
sampling (useless) for the display with respect for these restrictions.
Note Volume preview remains displayed even after the closure of the dialogue box. It is possible to
remove it from the display by deselecting the Show Preview box.
Preview by (high resolution) Slice is only available if the ART reconstruction is not
selected in Preferences. Preview by Slice is accessible regardless of the tab displayed
at the bottom of the dialogue box.
Launching the reconstruction:
 Select the button. This allows the reconstruction of a slice arbitrarily

placed in a greater resolution (1024 x 1024 by default). The position and
orientation of this slice can be set in the dialogue box by specifying a Plane
Centre Point and a normal to this plane (Plane Normal). It can also be set by
the normal cutting plane, which can be manipulated in 3D display, for
example, on a low resolution volume preview.
Note The successive slice previews open a new display window each time to
allow comparisons between the different slices/versions.
Note The user can interactively edit the window’s title to a more appropriate comment
(using the modified parameters), for example, by default, the title re-uses the
position of the calculated slice.
Figure 6–60: illustrates two 1024 x 1024 slices calculated with two sub-
collections of different radiographs.
Figure 6–60: Preview of a 1024 x 1024 Pixel Slice: (Left) 36 Radiographs (Right)
180 Radiographs
This illustrates the importance of the number of radiographs used and their resolution
on the quality of previews. The slice on the left has been calculated based on 36
images (reusing the same cache as the precedent volume preview). The slice on the
right has been calculated based on 180 images (one out of two).
6.4.8.2 Adjust
Although geometric parameters or beam hardening coefficient can be finely adjusted
through previews, in practice, it can be tedious to wait for the end of the calculations of
multiple iterations on a given value. It is also impossible to acquire a sufficiently
accurate preview, particularly because of memory limitation, which prevents the use of
all the full resolution radiographs available in the preview cache.
Figure 6–61: Parameters List
Figure 6–62: Adjustment Tab GUI
A semi-automatic tool is proposed (see Figure 6–62:).The user selects which

variable they want to make the adjustments. The parameter increment must be set up
(step). Selecting the Recompute button enables the software to compute the slices
defined in the Preview Settings tab.
It uses the following parameter values:
• Init_value - increment
• Init_value
• Init_value + increment
The resulting slices are displayed in the main window.
Note For the first step, the initial value used corresponds to the one set up in the
geometry definition tab.
Figure 6–63: Examples of Z Slices Corresponding to the Centre of Rotation

Positions (-0.05,0,0), (0,0,0) et (0.05,0,0) from Left to Right
When processing is complete, to inform which new value to take, one has to click on
the radio button corresponding to the best reconstructed slice. The aim is to set the
best image in the centre of the different views and select the Accept Geometry button
to update the geometry dialogue tab.
6—42
6.5 Analysis of Cutting Planes: DigiCUT Plug-In
As with all plug-ins in the MuriSlice software suite, DigiCUT is protected by a

software key.
6.5.1 General Presentation of DigiCUT
The Cutting Plane Analyzer command allows a 2D cutting plane to be visualised and
analysed (see Figure 6–64:).
The Cutting Plane Analyzer icon can be found in the plug-ins’ button bar or
alternatively, Tools -> Cutting Plane Analyzer from the main menu.
Figure 6–64: Cutting Plane Analysis Dialogue Box
6.5.2 DigiCUT Functionalities
6.5.2.1 Resolution
Image size and pixel size are set into the Resolution area. It allows the modification of
pixel dimensions in millimetre and image resolution in pixels.
6.5.2.2 Contrast
Contrast can be set using white/black/gamma buttons. The Volume Contrast button
fixes the image contrast using the 3D volume histogram range.
6.5.2.3 Moving in the Image
The Zoom zone is composed of 4 buttons and 4 arrows:
Zoom Zone Buttons

Fit Adjusts the size of the image to the window size
1:1 Adjusts the size to the scale of 1:1 (1 image pixel

corresponds to 1 screen pixel)

All rights reserved. 8/9/14 6—43
Zoom Zone Buttons

. Centres the image in the window
4 Arrows Moves the image in the window
+/- Zoom +/-
The user can zoom in on precise rectangles by holding down the shift key, clicking
the left mouse button, then moving and releasing the button.
6.5.2.4 Other Features

Right clicking Slice Image displays the features menu:
• Help; displays the Help window of commands and shortcuts

• Save Image; saves the current image
• Close; closes the window
• Level Curve Mode; activates the density profile examination mode
• Measure Mode; activates the measure mode
6.5.2.4.1 Level Curve Mode

During the analysis of a density profile, the line being analysed is marked by a green
line (see Figure 6–65:)—left clicking the mouse will move the green line. The user
can switch the analysis (the horizontal or vertical line) by ticking/not ticking the
vertical box in the contextual menu. The data can be exported in Excel format by
using the Export Curve Data command in the contextual menu.
Figure 6–65: Example of Density Profile Analysis
6—44
6.5.2.4.2 Measures
Right clicking Measure Mode displays a button bar which provides multiple types of
measures (see Figure 6–66), for example, the precision of the pixel.
Note The Measure tool proposes informative measure, however it doesn’t claim to provide a
precise measure as a metrology software. The expected precision will be in relation to
the position of the mouse click and to the resolution of the image.
Figure 6–66: Proposed Measures
Note It is possible to refine the position of the selected points (see Figure 6–66:).
6.5.2.4.3 Measure Reference

The required information for Reference can be found in section 6.3.3.2

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6.5.2.4.4 Point
To select a point within an image:
 Select a point to measure within an image and left click on a desired pixel
Displayed information:
• X, Y, Z location in measured reference
• Corresponding grey level in the pixel
Figure 6–67: Points Measure
6—46
6.5.2.4.5 Length Measure

There are two methods available for measuring length.
Method 1: Measuring length:
1. Select segment measure and verify assisting mode is deactivated

2. Left click the mouse to select the origin point of the segment
3. Left click the mouse to select the end-point of the segment. Segment limits
are represented by small squares.
Method 2: Measuring length:
1. Select segment measure
2. Select assisting mode

3. Left click the mouse near the desired origin point of the segment.
4. Left click the mouse near the desired end-point of the segment.
The assisting mode integrates an edge detection tool based on the analysis
of grey-levels along the profile drawn by the segment. Segment extremities are
then adjusted to fit the real borders of the part one wants to measure. Segment
limits are represented with small vertical bars. The displayed information is
Segment length.
Figure 6–68: Segment Length Measure
6.5.2.4.6 Angle Measure

To select an angle within the image:
1. Select angle measure and left click the first point of angle definition
2. Left click to select the second point of angle definition
3. Left click to select the third point of angle definition
• The angle value between two segments is defined by first/second
points selected and second/third points selected.
6.5.2.4.7 Circle Measure

There are two methods available for measuring a circle.
Method 1: Measuring a circle:
1. Select circle measure and verify assisting mode is deactivated

2. Left click the mouse to select the circle center
3. Left click the mouse to determine circle radius
• Circle diameter
• Location of the center in the reference
• Perimeter value
• Disk area delimited by the circle
Method 2: Measuring a circle:
1. Select circle measure and assisting mode (can be deactivated)

2. Left click on 10 points (roughly defining a circle). When the 10th point is
selected, the circle will adjust to fit the object border.
• Circle diameter
• Location of the center in the reference
• Perimeter value
• Disk area delimited by the circle
6—48
6.5.2.4.8 Profile Measure

To measure a profile along a segment:
1. Select segment measure and profile edition

2. Measure the segment
Figure 6–69: Profile Measure: Illustration of Profile Edition
6.5.2.4.9 Other Functions

Properties edition of the measure is made by clicking the right clicking the mouse on
the point and selecting Properties (Figure 6–70:will display). The user can modify
the colour of the measure (Color), size of the text (Text Size), number of decimals
(Decimals), and widths of the lines of measure (Width).
Right clicking on a point will remove it or remove the measure.
Figure 6–70: Measure Example
6.5.3 Specific Slice Extraction Modules
DigiCUT plug-in only manages Cut Plane.
6.5.3.1 Cut Plane

The Cut Plane tab computes a 2D slice image from 3D object using cutting planes.
The Apply button computes the current cutting plane. To locate the cutting plane, the
user can fix the values of plane normal and plane centre filling Normal and Center
boxes. The user can also move the clipping plane in the 3D view by using the mouse
in clipping plane management mode.
The <<Back and Next>> buttons make the cutting plane move along the normal
axes (direction) with a moving step equal to Thickness. Views are automatically
recomputed. The Stack As button grabs a set of images from the top of the volume
to its end along the normal axes (direction). The Slice As button grabs only the
current displayed slice.
Note The step between two slices is fixed by Thickness (value).
6—50
6.6 Automation of Reconstruction Tasks: Batch Mode
As with the other plug-ins in the MuriSlice software suite, the batch mode is
protected by a software key.
6.6.1 General Presentation
MuriSlice offers the user the possibility of carrying out a group of tasks
automatically and without supervision. Batch mode consists of writing a small
command script, which requests the execution of basic tasks, such as
reconstruction, display or even other functions.
6.6.2 Batch Mode Functioning
To access batch mode:
 Select Windows Script menu . The script window (Figure 6–71) will display.
Note The list of basic menu functions can be obtained by clicking Help in the script
window and then selecting the Go button.
Figure 6–71: Script Window
Figure 6-73 illustrates a script example, which allows:

• Loading a calibration file
• Requesting a reconstruction with interpolation of the voxels
• Setting the final resolution at 256 x 256 x 256
• Launching the reconstruction via DigiFDK
• Displaying the volume in DigiOBS
Clicking the Go button will execute the script.
Figure 6–72: Example of Script Programme
Section 7: Active DCAM Manual Xstrahl SARRP Operator Manual
Section 7:
Active DCAM Manual
in this section
7.1 Active DCAM Overview ................................................................................ 1
7.2 Driver Setup ……………………………….......................................................... 4
7.3 1394b (FireWire 800) ................................................................................... 11
7.4 Registration ................................................................................................. 19
7.5 User Interface .............................................................................................. 41
7.6 Properties Dialogue Box …………………………............................................. 49
7 Active DCAM Manual

7.1 Active DCAM Overview
This section demonstrates how to use the Active DCAM software that works with the Portal
Camera. The user is able to adjust multiple camera parameters in real time such as brightness,
aim, shutter, camera, sharpness, view, saturation and white balance.
Xstrahl SARRP Operator Manual Section 7: Active DCAM® Manual
7.2 Driver Setup

In order for ActiveDcam to recognize 1394 digital cameras that are connected to your
system, DCAM 1394 Camera Driver must be installed for each camera. This chapter
explains how to install the driver in your system under the Windows
2000/XP/Vista/Windows 7 operating system. If your 1394 camera comes with its own
DCAM-compatible system software, do not use it, as it will not be compatible with
ActiveDcam .
To install DCAM 1394 Camera Driver, perform the following steps:
7.2.1 Installation
1. Make sure ActiveDcam is installed on your system. Connect your camera to the
1394 (FireWire) port. If no driver was previously installed for the camera, the Found
New Hardware dialog will appear as shown below.
If the dialog does not show up, proceed to section 4 .
2. Choose not to connect to Windows Update and click Next. On the next dialog
select Install the software automatically. Ignore the warning message that the
driver is not signed up with Microsoft and click Continue Anyway.
3. Click Finish to complete the installation of the DCAM 1394 Camera Driver for the
selected camera. Verify that your camera is now listed in the device manager
as DCAM-compliant 1394 Camera :
4. If the New Hardware Found dialog didn't appear after you connected your camera,
go to the Start menu -> Programs -> ActiveDcam and select Install Camera Driver.
This should install the driver for all DCAM-compliant cameras connected to your
system. Ignore the warning messages that the driver is not signed up with
Microsoft.
5. As an alternative to the automatic installation, you can install the driver manually.
Right click on My Computer and click Properties. Select the Hardware tab and
click Device Manager. If there is no compatible driver installed, your camera will
appear in the device list as a Generic 1394 Camera with a question or exclamation
mark next to it:
If the system already has a compatible third party driver installed, the camera will
appear under Imaging Devices with the third party driver's name next to it:
In order for the camera to work properly with ActiveDcam software, its driver must
be changed to DCAM 1394 Camera Driver.
6. Right click on your device and select Properties . Choose the Driver tab and then
click Update Driver .
7. Select either Install from a list or specific location (Windows 2000/Windows XP)
or Browse my computer for driver software (Windows Vista/Windows 7) and
click Next .
8. Select either Don't search, I will choose the driver to install (Windows
2000/Windows XP) or Let me pick from a list of device drivers on my
computer (Windows Vista/Windows 7) and click Next . On the next dialog,
click Have disk.
9. Provide the path to ActiveDcam subfolder containing a camera driver for your
operating system. A typical location would be:
Windows 2000/XP/Vista/Win 7 C:\Program Files\ActiveDcam\Driver\Win32
Windows XP/Vista/Win 7 64-bit C:\Program Files\ActiveDcam\Driver\Win64

Windows Server 64 bit
10. From the list of the drivers select DCAM-compliant 1394 Camera and click Next .
Ignore the warning message that the driver is not signed up with Microsoft:
11. Click Finish to complete the installation of DCAM 1394 Camera Driver for the
selected camera. Verify that your camera is now listed in the device manager
as DCAM-compliant 1394 Camera.
The driver installation is now complete. You might need to restart the system for the
changes to come into effect.
Note - the described procedure must be repeated for each DCAM-compliant camera
that you intend to use with ActiveDcam, regardless of a manufacturer or model.
Note - ActiveDcam supports only those cameras that comply with IIDC 1394-based
Digital Camera Specification. DV camcorders and some other cameras that have
the 1394 (FireWire) physical interface, but are not DCAM-compliant will not be
recognized by ActiveDcam.
7.3 1394b (FireWire 800)
ActiveDcam supports 1394b cameras that can operate at 800 Mbps. In order to run 1394b
cameras at full capacity, you should use a 1394b (FireWire 800) PCI or PCMCIA card and 9-pin to
9-pin 1394b cable.
Microsoft Windows 2000 and Windows XP SP1 support 800 Mbps through a built-in OHCI IEEE-
1394 driver. However, with the release of Windows XP SP2 and SP3 Microsoft introduced a bug
that limited the speed of 1394b devices to 100 Mbps. Microsoft later released a Hotfix 885222 that
provided a partial solution to the problem:
Applying the Hotfix increases the speed of 1394 bus to 400 Mbps, but it still fails to provide 800
Mbps required for 1394b cameras. As a workaround to this issue, you need to "rollback" to 1394
OHCI drivers that come with Windows XP SP1. To perform a rollback, do the following steps:
1. Make sure Microsoft Hotfix KB885222 is not installed. Go to Control Panel, Add or
Remove Programs, select Show Updates, and remove this update if installed.
2. Rename sp2.cab (found in the C:\Windows\Driver Cash\i386 folder) to something like
sp2_old.cab, so Windows will not find it. If you have Service Pack 3 installed, rename
sp3.cab to sp3_old.cab.
3. Unplug your 1394 camera(s). Right click on My Computer and click Properties.
Select the Hardware tab and click Device Manager. Under IEEE 1394 Bus host
controllers locate your 1394b card driver. It will typically be listed as OHCI Compliant
IEEE 1394 Host Controller or Texas Instrument OHCI Compliant IEEE 1394 Host
Controller:
4. Right click on the device and select Properties . Choose the Driver tab and then
click Update Driver.
5. Select Install from a list or specific location and click Next . Then select Don't
search, I will choose the driver to install and click Next . On the next dialog,
click Have disk.
6. Provide the path to ActiveDcam Driver folder where 1394.inf is located (typically
C:\Program Files\ActiveDcam\Driver).Click OK :
7. From the list of the drivers select OHCI Compliant IEEE 1394 Host Controller and
click Next. Ignore the digital signing warnings and messages about installing the
older version of the driver.
8. Click Finish to complete the installation. To make sure the "rollback" procedure
worked, go to Device Manager, right click on OHCI Compliant IEEE 1394 Host
Controller, select Properties. Choose the Driver tab and then click Driver Details.
Confirm that 1394bus.sys and ohci1394.sys files have file version 5.1.2600.1106:
9. Rename sp2x.cab back to sp2.cab. If you have Service Pack 3 installed, rename
sp3x.cab back to sp3.cab. Plug in your camera(s). If DCAM-compliant 1394
camera does not appear under Imaging Devices, repeat camera driver installation
according to Driver Setup section. You might need to restart the system for the
changes to come into effect.
Note - you will only need to perform the rollback if you have Windows XP SP2 or SP3 installed on
your system. Windows 2000 and Windows XP SP1 will support 1394b out-of-the-box. For 1394b
support in Windows Vista you will need to install a special driver which can be provided upon
request.
Note - Windows Vista does not natively support 1394b at 800 mbps. However, some third-party
OHCI drivers compatible with ActiveDcam are available. Contact your vendor for more
information.
Note - Windows supports 1394b at 800 mbps out-of-the-box. No additional actions are required to
run ActiveDcam with 1394b cameras on Windows 7, both 32- and 64-bit versions.
7.4 Registration
The ActiveDcam setup includes the demonstration license that allows you to use the
control in both design and run-time mode for a period of 21 days.
If you wish to continue using the control, you must acquire a design-time license from
your distributor. The design-time license is provided in form of a license
file activedcam.lic that must be saved in the ActiveDcam folder (typically, C:\Program
Files\ActiveDcam) replacing the existing file. In addition, if you need to execute
ActiveDcam based applications outside of your VB development environment, you
should perform a run-time registration. This is done through the following procedure.
When you first start an executable file that was created using ActiveDcam, the
registration dialog box will appear.
The dialog will display a Control ID uniquely generated for your system. Based on this
ID, your distributor will provide your with a Serial Number that will validate a run-time
permission for ActiveDcam. After the proper Serial Number is entered in the dialog and
registration completed, all ActiveDcam based application will become unlocked.
7.5 User Interface
Dcam Viewer is a universal plug-and-play application for DCAM (IIDC-1394) compliant

cameras which is intended for camera and CPU performance evaluation. It can display
live video from multiple cameras, provide full control over camera parameters, analyze
incoming video frames and save them to image files. DcamViewer is available only as
a part of ActiveDcam SDK and not as a separate distribution.
To start DcamViewer run “DcamViewer.exe” from ActiveDcam working folder. You can
also run it throught the Windows Start Menu: Start -> All Programs -> ActiveDcam ->
Dcam Viewer or by double-clicking on the DcamViewer icon on the desktop. The
following user interface will be displayed:
Figure 1: DCAM User Interface
When DcamViewer is launched for the first time, it will attempt to connect to the first
camera in the DCAM-compliant camera list and start acquiring the live video.
Toolbar
The most often used commands to operate the viewer are provided through the toolbar
at the upper part of the application window:
Live Video
Switches the camera into the continuous acquisition mode and initiates the live
preview.
One Shot
Initiates an acquisition of one frame.
Save Image
Let’s you save the current frame buffer in an image file. When you click this
button, the Save As dialog box will appear where you can select the file name
and one of the image file formats: BMP, TIF and JPEG.
Open Image
Let’s you open the static image from a file and display the image. When you
click this button, the Open dialog box will appear where you can select the file
name and one of the image file formats: BMP, TIF and JPEG.
Zoom In
Click this button to increase the magnification of the image.
Zoom Out
Click this button to decrease the magnification of the image.
Fit to Screen
Click this button to change the magnification factor of the image so that it fits to
the image window.
Full Screen
Click this button to enter the full screen mode. To exit the full screen mode,
press the Esc key or double-click on the image.
Settings
Click this button to display ActiveDcam Property Pages.
In addition to the buttons, the toolbar also contains the following contents:
Frame Rate
Show the current frame rate of the camera in frames per second.
Select Camera
Use this option to switch between several connected cameras.
Select Format
Use this option to select the desired pixel format from the list of available
formats.
Select Frame Rate

Use this option to set the desired frame rate for the camera.
Status Bar
The Status Bar appears along the lower edge of DcamViewer window and contains the
following information fields in the order from left to right:
Frames acquired
Displays the amount of acquired frames since the last restart of the acquisition.
Frames skipped
Displays the amount of skipped frames since the last restart of the acquisition.
Image Size
Displays the horizontal and vertical size of the video frames.
Cursor Position
Displays the X and Y coordinates of the mouse pointer. The coordinates are
expressed in pixels relative to the top left corner of the image.
Pixel Value
Displays the values of the pixel identified by the mouse pointer. For a
monochrome image, each pixel value will be represented by a single number,
while for an RGB image by a triad of numbers.
Menu
Right-clicking the video window of DcamViewer will display the context menu with the
following commands:
Acquire Video
Switches the camera into the continuous acquisition mode and initiates live
preview. Equivalent to pressing the Live button.
Store Camera Parameters

Selecting this option will make DcamViewer store the main camera parameters
upon its exit and restore them upon the next start. The parameters of each
camera are stored independently in the system registry.
Settings
Displays ActiveDcam Property Pages.
Save Image
Allows you to save the current frame buffer in an image file.
Open Image
Allows you to open the static image from a file.
Zoom In
Increases the magnification of the image.
Zoom Out
Decreases the magnification of the image.
Fit to Screen
Changes the magnification factor of the image so that it fits to the image
window.
Operation
You can run several instances of DcamViewer at the same time provided each instance
of the viewer is connected to a different camera.
If you want the current parameters of the camera to be memorized, active the Store
camera parameters option from the context menu. DcamViewer will save the
parameters of the camera in the system registry upon exiting and restore it next time
this camera is selected.
7.6 Properties Dialogue Box
The following property pages are available in ActiveDcam control:
Source Used to select the properties specifying the source for the video input
Format Used to select the properties specifying the format of the video
Exposure Used to select the properties specifying the exposure features of the
video
Color Used to select the properties specifying the color features of the video
Advanced Used to select the properties specifying the advanced features of the
video
Display Used to select the properties specifying the display settings
7.6.1 Source
This property page is used to select the properties specifying the source for the video
input.
Select from the following options:
Camera
Displays the vendor's name and model of the currently selected camera. If you have
more than one camera connected to the 1394 board, you can switch to another
camera by choosing the corresponding camera name in the list. Equivalent to
the Camera property.
Acquire
Allows you to enable the continuous acquisition mode. If this box is checked, the
board will continuously acquire the video into the internal image memory. If the control
is visible, the live video will be displayed in the control window. Equivalent to
the Acquire property.
Asynchronous mode
Allows you to select an acquisition mode. Check this box to set the board to the
asynchronous mode. In this mode the board will continuously transfer pixels into the
host memory, allowing your application to process a captured frame while the
acquisition of the next frame occurs. The asynchronous mode provides the fastest
and most efficient setup for real-time image processing. However, if processing
occurs at a slower rate than pixels are acquired, using this mode may result in the
decomposition of images and loss of data. Clear this check box to set the board to
the synchronous mode. In this mode the acquisition of the next frame will be initiated
upon the capture command. The synchronous mode is slower, but it guarantees the
wholeness of images during real-time processing. Equivalent to the Asynch
property.
Timeout
Use this option to set the number of seconds to wait for a frame to be acquired.
Typically used to assign the timeout when the Trigger mode is active. If the timeout
expires, the Timeout event event will be raised. Equivalent to the Timeout property.
ISO speed
Allows you to choose the camera's isochronous transmission speed in Mbps/sec.
Possible values are 100, 200, 400 for 1394a cameras and 100, 200, 400, 800 for
1394b cameras. By default the transmission speed is set to the maximum value
available for the current 1394 configuration. Reducing the transmission speed can be
useful in multiple cameras situations in order to limit the bandwidth available to each
camera. Equivalent to the SetIsoSpeed method.
Trigger
Select this check box to set the current camera to the trigger mode. This mode is
typically used with an asynchronously resetable camera. The acquisition of a frame
will occur upon receiving a signal from an external hardware trigger. To set the
camera to the continuous mode, clear the Trigger check box. Equivalent to
the Trigger property.
Trigger Source
Allows you to select the source for the trigger signal. Depending on a camera, there
may be one or more hardware trigger inputs as well as the software trigger. If the
software trigger is available and selected, use the Set button to set and reset the
trigger event. If the camera doesn't suppot trigger source selection as defined by the
DCAM 1.31 specifications, this option will be unavailable. Equivalent to
theTriggerSource property and SoftTrigger method.
Trigger mode
Allows you to select the trigger mode as defined by the DCAM 1.31 specifications. If
several trigger modes are available for the currently selected camera, you can switch
between them by choosing the desired mode from the list. See TriggerMode for more
details.
Trigger polarity
Allows you to change polarity of the trigger input. Equivalent to
the TriggerPolarity property. Choose one of the following options:
High Active - trigger has high active input.
Low Active - trigger has low active input.
Trigger counter
Allows you to select the trigger counter (trigger parameter) as defined by the DCAM
1.31 specifications. Equivalent to the TriggerCounter property. See TriggerMode for
more details on the usage of the trigger counter.
Trigger delay
Allows you to select the raw value for the trigger delay which defines the time
between the arrival of the trigger signal and acquisition of the frame. Equivalent to
the TriggerDelay property.
7.6.2 Format
This property page is used to select the properties specifying the format and
synchronization options of the video.
Video mode
Use this option to select the desired video mode from the list of modes available for
the current camera. In addition to standard modes defined by the DCAM 1.31
specifications, camera-dependent partial scan modes (Format 7) can be available at
the bottom of the list. Each partial scan mode retains the frame size and packet size
previously selected for it. However, selecting the same partial scan mode twice will
reset its parameters to maximum values, thus providing the highest resolution and
frame rate available for the mode.Equivalent to the Mode property.
Frame rate
Allows you to choose the frame rate available for the currently selected Mode. Select
among the following possible frame rates: 1.875 fps, 3.75 fps, 7.5 fps, 15 fps, 30 fps,
60 fps. If one of the partial scan modes (Format 7) is selected, this option will be
unavailable, as the frame rate will depend on the size of the scan window and Packet
size. Equivalent to the Rate property.
Packet size
Use this option to select the number of bytes in an isochronous packet. This option is
available only for partial scan (Format 7) modes and related but not necessarily
indicative of the effective frame rate. Equivalent to the PacketSize property.
Partial scan
Allows you to change the size and position of the image window in a partial scan
(Format 7) mode. To modify the size and position of the window, enter the desired
values for the image width, height, left coordinate and top coordinate in pixels.
Equivalent to the SizeX, SizeY, StartX, StartY properties.
16-bit swap
Select this box to change the order of bytes in incoming camera frames. While
outputting 16-bit pixels, some cameras can place the most significan bits of each
pixel in the high-order bytes and the least significant bits in the low-order bytes. If this
happens, the live image will appear scrambled. Checking this box will restore the
original pixel values. Equivalent to the SwapBytes property.
16-bit shift
Select the number of positions for the right bit shift to be applied to 16-bit pixel
values in the image buffer. When displaying and saving 16- and 48-bit
images, ActiveDcam assumes that pixel values are mapped to the entire 16-bit
dynamic range (0-65535). Certain cameras however may output data in narrower
dynamic range resulting in dark images. Selecting a non-zero bit shift will cause
real-time remapping of image data. Equivalent to the BitShift property.
7.6.3 Exposure
This property page is used to select the properties specifying the display features of the
video.
Brightness
Move the slider to adjust the brightness (black level) of the video. Note that this
option is available only for the cameras that support the software brightness
control.. Equivalent to the Brightness property.
Shutter
Move this slider to adjust the integration time of the incoming light. Note that this
option is available only for the cameras that support the software shutter control.
Equivalent to the Shutter property.
Gain
Move this slider to adjust the camera circuit gain control. Note that this option is
available only for the cameras that support the software gain control. Equivalent to
the Gain property.
Iris
Move this slider to adjust the iris (mechanical apperture) of the camera lens. Note that
this option is available only for the cameras that support the software iris control.
Equivalent to the Iris property.
Gamma
Move the slider to adjust the gamma level of the video. The gamma correction
modifies an image by applying standard, nonlinear gamma curves to the intensity
scale. To lighten an image and increase the contrast in its darker areas, increase
the gamma by moving the slider to the right. To darken the image and emphasize
the contrast in the lighter areas, decrease in the gamma by moving the slider to the
left. Note that this option is available only for the cameras that support the software
gamma control. Equivalent to the Gamma property.
Sharpness
Move the slider to adjust the sharpness of the video. Note that this option is
available only for the cameras that support the software sharpness control.
Equivalent to the Sharpness property.
Optical Filter
Move the slider to adjust the optical filter of the camera. Depending on the camera
model, it can control the mechanical optical filter or the electronic filter. For Bayer
cameras this feature will typically allow for changing the color pattern of the raw
output data. Note that this option is available only for the cameras that support the
software sharpness control.. Equivalent to the OpticalFilter property.
Each of the sliders has a corresponding check box On located on the left
and Auto located on the right. If an On box is unselected, the corresponding feature will
be disabled. If an Auto box is enabled, the camera supports an automatic mode for the
corresponding feature. Checking the box will put the camera to the continuous
automatic control of the feature, unchecking it will restore the manual control.
Auto Exposure Reference

Use this option to control the AE mode of the camera. When the auto exposure mode
is activated, the camera will automatically control the exposure by
keeping Shutter, Gain and/or Iris at optimal levels. The reference value for auto
exposure can be adjusted by moving the slider next to the check box. Both options
are available only if the currently selected camera supports auto exposure control.
Equivalent to the AutoExposure and AutoExposureRef properties.
7.6.4 Color
synchronization options of the video.
Saturation
Move the slider to adjust the color saturation of the video. Note that this option is
available only for the cameras that support the software saturation control..
Equivalent to the Saturation property.
Hue
Move the slider to adjust the color phase the video. Note that this option is available
only for the cameras that support the software hue control.. Equivalent to
the Hue property.
Both sliders have a corresponding check box On located on the left and Auto located on
the right. If an On box is unselected, the corresponding feature will be disabled. If
an Auto box is enabled, the camera supports an automatic mode for the corresponding
feature. Checking the box will put the camera to the continuous automatic control of the
feature, unchecking it will restore the manual control.
White balance
Move the U/B slider to adjust the tint of the white color along the yellow-blue axis.
Move the V/Rslider to adjust the tint of the white color along the cyan-red axis.
Select the Auto box to put the camera to the continuous automatic control of the
white balance. Click the One Push button to have the camera adjust the white
balance level by itself and return to the manual mode. Equivalent to the
WhiteBalanceUB, WhiteBalanceVR and WhiteBalanceControl properties.
Bayer conversion
Select this option to activate the real-time color conversion of a grayscale video
generated by a Bayer camera. The Bayer list lets you select the specific Bayer
conversion algorithm. The CCD layout of the camera can be selected from
the Layout list. Both options are available only for monochrome video modes.
See Bayer and BayerLayout for more information.
Gains (R, G , B , Y)
Allows you to adjust the gain factors for individual color channels or the intensity
factor for a monochrome video. Equivalent to the SetGains property.
Palette
Allows you to select one of a few predefined palettes to be applied to a grayscale
live video. The palettes represent choices that may be useful in viewing different
kinds of video in pseudo-colors. Choose among the following palettes:
Gray
Applies the standard 256-level grayscale palette. This is a regular mode of
viewing a grayscale video.
Inverse
Applies the inverted 256-level grayscale palette. The video will be displayed in
the negative format.
Saturated
Applies the grayscale palette with colorized upper entries. The saturated palette
allows you to control the dynamic range of the video signal by bringing it slightly
below the saturation level of the video camera or video amplifier. To achieve the
maximum dynamic range, adjust the intensity of the light source and/or the gain
and zero level of the video amplifier so that the red color corresponding to the
brightest pixel values just barely shows up.
Rainbow
Applies a color palette where the entries are evenly distributed along the Hue
axis. This allows for assigning different color pigments to different levels of
intensity.
Spectra
Applies a color palette where the entries are distributed along the Hue and
Luminance axes. That allows for assigning different color pigments to different
levels of intensity while preserving the luminance scale.
Isodense
Applies the 256-level grayscale palette, each 8-th entry of which is colorized.
The isodense palette allows you to clearly see transitions between different
levels of intensities as isolines on a topographic map.
Multiphase
Applies the multiphase palette. Entries in the multiphase palette are at opposite
ends of the color model so even small changes in gray levels are highlighted.
Random
Applies the random color palette whose entries are filled with random values
each time you select it from the list.
7.6.5 Advanced
synchronization options of the video
Pan
Move the slider to adjust the pan of the camera. Depending on the camera model, it
can control the mechanical pan by physically moving the camera in the horizontal
plane or the electronic pan by choosing the horizontal position of the effective image
area on a CCD sensor. Note that this option is available only for the cameras that
support the software focus control.. Equivalent to the Pan property.
Tilt
Move the slider to adjust the tilt of the camera. Depending on the camera model, it
can control the mechanical tilt by physically moving the camera in the vertical plane
or the electronic tilt by choosing the veritcal position of the effective image area on a
CCD sensor. Note that this option is available only for the cameras that support the
software focus control.. Equivalent to the Tilt property.
Focus
Move the slider to adjust the camera lens to the subject distance. Note that this
option is available only for the cameras that support the software focus control..
Equivalent to the Focus property.
Zoom
Move the slider to adjust the optical zoom of the camera lens. Note that this option
is available only for the cameras that support the software zoom control.. Equivalent
to the Zoom property.
Each of the sliders has a corresponding check box On located on the left and Auto located
on the right. If an On box is unselected, the corresponding feature will be disabled. If
an Auto box is enabled, the camera supports an automatic mode for the corresponding
feature. Checking the box will put the camera to the continuous automatic control of the
feature, unchecking it will restore the manual control.
Register
Allows you to perform asynronous reads and writes to a selected register in the
camera 1394 address space. To perform the read operation, enter the desired
hexadecimal offset to the Offset filed and click the Read button. The offset should
be given relative to the 1394 base address FFFF:00000000 h. The result will be
displayed in the Hex Value box. To perform the write operation, enter a desired
offset and 32-bit hexadecimal value to the Offset and Hex Value fields
respectively, and then press the Write button. Use the Refresh button to
synchronize ActiveDcam properties with possible changes in the camera settings
that might have occured after changing the values of 1394 registers. Equivalent to
the ReadRegister, WriteRegister and LoadChannel methods.
Memory channel
Select the internal EEPROM channel for loading or storing camera settings. Use
the Save button to write the current setting to the internal camera memory. Use
the Load button to load the settings from the internal memory. Channel 0
corresponds to the default factory settings and cannot be overwritten. Equivalent to
the LoadChannel and SaveChannel methods.
Save image
Allows you to save the current frame buffer in an image file. When you click this
button, the Save As dialog box will appear where you can select the file name and
one of the image file formats: BMP, TIF and JPEG. Note that BMP and TIF files will
be recorded with no compression while JPEG files will be recorded with quality 75.
Equivalent to the SaveImage method.
7.6.6 Display
This property page is used to select the properties specifying the display settings
of ActiveDcam.
Display
Allows you to enable or disable live display in the control window. You might want to
disable the display option if you want to render captured frames by other means
such as Picture box. When using DirectShow Video Capture Filter, setting this
property to TRUE will activate the internal RGB24 conversion which is required by
image data access and image analysis methods. Equivalent to the
Display property.
Anti-tearing
Allows you to enable or disable the anti-tearing feature. Anti-tearing removes
horizontal tears in the live video caused by a difference between the camera frame
rate and refresh rate of the monitor. Equivalent to the AntiTearing property.
Monitor Sync
Allows you to enable or disable the monitor synchronization mode. If this box is
checked, the camera frame rate will exactly match the refresh rate of the system
monitor thus eliminating all the display artifacts related to the digital image transfer.
Equivalent to the MonitorSync property.
Scroll bars
Allows you to enable or disable the scroll bars in the control window. If this box is
checked and the video width or/and height exceed the size of the control window,
the scroll bar(s) will be displayed on the border of the control window allowing you
to pan the live video. Equivalent to the ScrollBars property.
Digital zoom
Allows you to adjust the magnification of the live video display. This option doesn't
change the content of the image data, but only its appearance in the control
window. If it is set to zero, the image will be fit to the size of the control window. In
this case the display might not retain the original proportions of the video frame.
Equivalent to the Magnification property. Note - if the Display option is unchecked
and Digital zoom is set to zero, ActiveDcam will enter a raw image transfer mode
with the minimal CPU usage.
Flip
Allows you to select one of the flipping modes. Flipping affects the live video display
as well as actual order of pixels in the frame buffer. Select among the following
modes:
Off
No image flipping is performed.
Horizontal
The image is flipped horizontally.
Vertical
The image is flipped vertically.
Diagonal
The image is flipped horizontally and vertically.
Rotate
Allows you to rotate the image. Rotation affects the live video display as well as
actual order of pixels in the frame buffer. Select one of the following modes:
Off
No image rotation is performed.
90°
The image is rotated counterclockwise.
180°
The image is rotated 180 degrees.
270°
The image is rotated clockwise.
Integrate Mode
Allows you to select the frame integration operation mode. The frame integration
allows you to average or add frames "on the fly" without sacrificing the frame rate.
Equivalent to the Integrate property. Select one of the following modes:
None
Frame integration is disabled.
Average
Running Average mode. Each output frame is the result of averaging a selected
number of previously captured frames.
Add
Running Accumulation mode. Each output frame is the sum of a selected
number of previously captured frames.
Integrate Window (N)
Sets the number of frames for the integration. Equivalent to
the IntegrateWnd property.
Hot Pixel Correct

Allows you to enable or disable the hot pixel correction mode. If this box is checked,
unusually bright pixels will be effectively removed from the image. Hot pixels are
assosiated with elements on a camera sensor that have higher than normal rates of
charge leakage. For more details on hot pixel correction refer to HotPixelCorrect.
Hot Pixel Level (%)
Sets the hot pixel correction level, in percent. Equivalent to
the HotPixelLevel property.
Background name
Let’s you enter the name prefix under which the background files are stored.
See BkgName for more details.
Save Dark
Click this button to store a dark field background image on the hard drive. Dark field
should be saved when no light transmitted through the camera lens. The dark field
will be calculated by averaging the number of consecutive frames specified by
the Frames option. Equivalent to the SaveBkg method.
Save Bright
Click this button to store a bright field background image on the hard drive. Bright
field should be saved with the maximum light transmitted and no objects in the field
of view. To achieve the best dynamic range, the light intensity should be adjusted
so that it stays just below the saturation level of the camera. To control the
saturation for monochrome cameras, use the Saturated Palette. The bright field will
be calculated by averaging the number of consecutive frames specified by
the Frames option.
Correct background
Allows you to select a background correction mode. Select None if you do not want
the background correction to be performed. Select Dark/Offset to apply the dark-
field background correction to each frame captured. Select Flat/Gain to apply the
flat-field background correction to each frame captured. Make sure to save the
bright and dark fields before using this option, otherwise certain background
correction modes will not be available. For more details on background correction
refer to BkgCorrect.
Appendix A:
Notes
FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company). 8/9/14
Worldwide
Gulmay Medical Inc.
480 Brogdon Road, Suite 300
Suwanee, GA 30024
t: +1 678 765 8970
f: +1 678 765 8975
e: support@xstrahl.com
w: www.xstrahl.com
Europe
Xstrahl Limited
The Coliseum
Watchmoor Park
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Camberly
Surrey GU15 3YL
t: +44 (0) 1276 462696
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SARRP

(Small Animal Radiation Research Platform)

Trademark Xstrahl® is a registered trademark of Xstrahl Limited.

Compliance The design of Xstrahl Systems is in compliance with internationally

Acknowledgments All manufacturer trade names and trademarks appearing in this

Glossary This following glossary explains the acronyms, abbreviations and

FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl company).

Sample Warning, Caution and Note:

WARNING: Warnings alert users to potential hazards to

CAUTION: Cautions alert users to the potential risk of

Note: A note provides important information about the related content.

These specific hazard notices are:

RADIATION: Xstrahl X-Ray systems generate ionising

HIGH VOLTAGE: High voltages are present in all

PROTECTIVE EARTH: Protective earth labels are

DANGER HIGH VOLTAGE; ISOLATE SUPPLY:

Intended Use (of equipment)

Xstrahl recommends this document be kept with the equipment at all

Document Amendment Table

1 Precautionary Information ....................................................................... (1—1)

5 SARRP Quick Start Guide ........................................................................ (5—1)

6 MuriSlice® Manual ................................................................................... (6—1)

6.4.1 Introduction ............................................................................................ (6—19)

7 Active DCAM Manual ............................................................................... (7—1)

Appendix A: Notes ...................................................................................... (A—1)

3 SARRP Control Interface Operator Manual

Examples of Irradiation Uses

SARRP Quick Start Guide

5 This section provides a quick overview of how to use the Xstrahl

• ImageJ User Guide

The SARRP system incorporates various safety features and components.

1.1 Ionising Radiation

1.2 Maintenance of Equipment

The SARRP is a small animal irradiation platform used in radiobiology

Figure 2–1: SARRP Main Operating Area

2.1 SARRP Modules

Figure 2–2: SARRP System

FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).

Figure 2–3: X-Ray Controller (MP1) Illustration

2.2 Safety System Interlocks

2.2.1 SARRP PC (Interface) and Supplementary

2.3 SARRP Training

FMSARRP Issue E ©2014 Gulmay Medical Inc. (an Xstrahl Company).

3 SARRP Control Interface Operator Manual

The SARRP Control Interface is a control software consisting of a main

The main interface (see Figure 3–1) performs the following

Figure 3–1: SARRP Control Interface Illustration

3.1 Robotic Specimen Stage Control

The SARRP provides 5º of freedom motion:

• 3 x translational stages for X, Y and Z motions of the animal specimen

Figure 3–2: User Interface

3.2 Homing the Stages

CAUTION: The robotic stage must be in the Origin position before

The software is capable of distinguishing whether homing is required or not. If

Figure 3–3: Homing: Rotational Stage Arrangement

Figure 3–4: Circular Gear Arrangement

3.2.1 Rotating the Entire Stage

3.2.2 Starting the Homing Sequence

3.3 Coordinate Systems

The SARRP system has two coordinate systems:

Figure 3–6: Robot Coordinate System

The user interface is designed to work primarily with the SARRP CT

Figure 3–7: User Interface with ISO and Gantry Selection

It is also possible to specify/display the position in the robot coordinate system